Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
apm(8)
control the APM BIOS and display its information
bios(9), bios_sigsearch(9), bios32_SDlookup(9), bios32(9), bios_oem_strings(9)
interact with PC BIOS
bus_dma(9), bus_dma_tag_create(9), bus_dma_tag_destroy(9), bus_dma_template_init(9), bus_dma_template_tag(9), bus_dma_template_clone(9), bus_dma_template_fill(9), BUS_DMA_TEMPLATE_FILL(9), bus_dmamap_create(9), bus_dmamap_destroy(9), bus_dmamap_load(9), bus_dmamap_load_bio(9), bus_dmamap_load_ccb(9), bus_dmamap_load_crp(9), bus_dmamap_load_crp_buffer(9), bus_dmamap_load_mbuf(9), bus_dmamap_load_mbuf_sg(9), bus_dmamap_load_uio(9), bus_dmamap_unload(9), bus_dmamap_sync(9), bus_dmamem_alloc(9), bus_dmamem_free(9)
Bus and Machine Independent DMA Mapping Interface
devstat(9), devstat_end_transaction(9), devstat_end_transaction_bio(9), devstat_end_transaction_bio_bt(9), devstat_new_entry(9), devstat_remove_entry(9), devstat_start_transaction(9), devstat_start_transaction_bio(9)
kernel interface for keeping device statistics
dpms(4)
VESA BIOS DPMS driver
g_new_bio(9), g_clone_bio(9), g_destroy_bio(9), g_format_bio(9), g_print_bio(9), g_reset_bio(9)
GEOM bio controlling functions
gptboot(8)
GPT bootcode for UFS on BIOS-based computers
gptzfsboot(8)
GPT bootcode for ZFS on BIOS-based computers
isoboot(8)
Boot code for hybrid ISO/USB images on BIOS-based computers
sglist(9), sglist_alloc(9), sglist_append(9), sglist_append_bio(9), sglist_append_mbuf(9), sglist_append_mbuf_epg(9), sglist_append_phys(9), sglist_append_sglist(9), sglist_append_single_mbuf(9), sglist_append_uio(9), sglist_append_user(9), sglist_append_vmpages(9), sglist_build(9), sglist_clone(9), sglist_consume_uio(9), sglist_count(9), sglist_count_mbuf_epg(9), sglist_count_vmpages(9), sglist_free(9), sglist_hold(9), sglist_init(9), sglist_join(9), sglist_length(9), sglist_reset(9), sglist_slice(9), sglist_split(9)
manage a scatter/gather list of physical memory addresses
smbios(4)
System Management BIOS
sym(4)
NCR/Symbios/LSI Logic 53C8XX PCI SCSI host adapter driver
zfsboot(8)
bootcode for ZFS on BIOS-based computers
BIO_ADDR(3), BIO_ADDR_new(3), BIO_ADDR_clear(3), BIO_ADDR_free(3), BIO_ADDR_rawmake(3), BIO_ADDR_family(3), BIO_ADDR_rawaddress(3), BIO_ADDR_rawport(3), BIO_ADDR_hostname_string(3), BIO_ADDR_service_string(3), BIO_ADDR_path_string(3)
BIO_ADDR routines
BIO_ctrl(3), BIO_callback_ctrl(3), BIO_ptr_ctrl(3), BIO_int_ctrl(3), BIO_reset(3), BIO_seek(3), BIO_tell(3), BIO_flush(3), BIO_eof(3), BIO_set_close(3), BIO_get_close(3), BIO_pending(3), BIO_wpending(3), BIO_ctrl_pending(3), BIO_ctrl_wpending(3), BIO_get_info_callback(3), BIO_set_info_callback(3), BIO_info_cb(3), BIO_get_ktls_send(3), BIO_get_ktls_recv(3)
BIO control operations
BIO_do_handshake(3), BIO_f_ssl(3), BIO_set_ssl(3), BIO_get_ssl(3), BIO_set_ssl_mode(3), BIO_set_ssl_renegotiate_bytes(3), BIO_get_num_renegotiates(3), BIO_set_ssl_renegotiate_timeout(3), BIO_new_ssl(3), BIO_new_ssl_connect(3), BIO_new_buffer_ssl_connect(3), BIO_ssl_copy_session_id(3), BIO_ssl_shutdown(3)
SSL BIO
BIO_f_base64(3)
base64 BIO filter
BIO_f_cipher(3), BIO_set_cipher(3), BIO_get_cipher_status(3), BIO_get_cipher_ctx(3)
cipher BIO filter
BIO_f_md(3), BIO_set_md(3), BIO_get_md(3), BIO_get_md_ctx(3)
message digest BIO filter
BIO_f_null(3)
null filter
BIO_find_type(3), BIO_next(3), BIO_method_type(3)
BIO chain traversal
BIO_get_buffer_num_lines(3), BIO_set_read_buffer_size(3), BIO_set_write_buffer_size(3), BIO_set_buffer_size(3), BIO_set_buffer_read_data(3), BIO_f_buffer(3)
buffering BIO
BIO_get_ex_new_index(3), BIO_set_ex_data(3), BIO_get_ex_data(3), ENGINE_get_ex_new_index(3), ENGINE_set_ex_data(3), ENGINE_get_ex_data(3), UI_get_ex_new_index(3), UI_set_ex_data(3), UI_get_ex_data(3), X509_get_ex_new_index(3), X509_set_ex_data(3), X509_get_ex_data(3), X509_STORE_get_ex_new_index(3), X509_STORE_set_ex_data(3), X509_STORE_get_ex_data(3), X509_STORE_CTX_get_ex_new_index(3), X509_STORE_CTX_set_ex_data(3), X509_STORE_CTX_get_ex_data(3), DH_get_ex_new_index(3), DH_set_ex_data(3), DH_get_ex_data(3), DSA_get_ex_new_index(3), DSA_set_ex_data(3), DSA_get_ex_data(3), ECDH_get_ex_new_index(3), ECDH_set_ex_data(3), ECDH_get_ex_data(3), EC_KEY_get_ex_new_index(3), EC_KEY_set_ex_data(3), EC_KEY_get_ex_data(3), RSA_get_ex_new_index(3), RSA_set_ex_data(3), RSA_get_ex_data(3)
application-specific data
BIO_get_new_index(3), BIO_meth_new(3), BIO_meth_free(3), BIO_meth_get_read_ex(3), BIO_meth_set_read_ex(3), BIO_meth_get_write_ex(3), BIO_meth_set_write_ex(3), BIO_meth_get_write(3), BIO_meth_set_write(3), BIO_meth_get_read(3), BIO_meth_set_read(3), BIO_meth_get_puts(3), BIO_meth_set_puts(3), BIO_meth_get_gets(3), BIO_meth_set_gets(3), BIO_meth_get_ctrl(3), BIO_meth_set_ctrl(3), BIO_meth_get_create(3), BIO_meth_set_create(3), BIO_meth_get_destroy(3), BIO_meth_set_destroy(3), BIO_meth_get_callback_ctrl(3), BIO_meth_set_callback_ctrl(3)
Routines to build up BIO methods
BIO_hostserv_priorities(3), BIO_parse_hostserv(3)
utility routines to parse a standard host and service string
BIO_lookup_type(3), BIO_ADDRINFO(3), BIO_ADDRINFO_next(3), BIO_ADDRINFO_free(3), BIO_ADDRINFO_family(3), BIO_ADDRINFO_socktype(3), BIO_ADDRINFO_protocol(3), BIO_ADDRINFO_address(3), BIO_lookup_ex(3), BIO_lookup(3)
BIO_ADDRINFO type and routines
BIO_new(3), BIO_up_ref(3), BIO_free(3), BIO_vfree(3), BIO_free_all(3)
BIO allocation and freeing functions
BIO_new_CMS(3)
CMS streaming filter BIO
BIO_printf(3), BIO_vprintf(3), BIO_snprintf(3), BIO_vsnprintf(3)
formatted output to a BIO
BIO_push(3), BIO_pop(3), BIO_set_next(3)
add and remove BIOs from a chain
BIO_read_ex(3), BIO_write_ex(3), BIO_read(3), BIO_write(3), BIO_gets(3), BIO_puts(3)
BIO I/O functions
BIO_s_accept(3), BIO_set_accept_name(3), BIO_set_accept_port(3), BIO_get_accept_name(3), BIO_get_accept_port(3), BIO_new_accept(3), BIO_set_nbio_accept(3), BIO_set_accept_bios(3), BIO_get_peer_name(3), BIO_get_peer_port(3), BIO_get_accept_ip_family(3), BIO_set_accept_ip_family(3), BIO_set_bind_mode(3), BIO_get_bind_mode(3), BIO_do_accept(3)
accept BIO
BIO_s_bio(3), BIO_make_bio_pair(3), BIO_destroy_bio_pair(3), BIO_shutdown_wr(3), BIO_set_write_buf_size(3), BIO_get_write_buf_size(3), BIO_new_bio_pair(3), BIO_get_write_guarantee(3), BIO_ctrl_get_write_guarantee(3), BIO_get_read_request(3), BIO_ctrl_get_read_request(3), BIO_ctrl_reset_read_request(3)
BIO pair BIO
BIO_s_fd(3), BIO_set_fd(3), BIO_get_fd(3), BIO_new_fd(3)
file descriptor BIO
BIO_s_file(3), BIO_new_file(3), BIO_new_fp(3), BIO_set_fp(3), BIO_get_fp(3), BIO_read_filename(3), BIO_write_filename(3), BIO_append_filename(3), BIO_rw_filename(3)
FILE bio
BIO_s_null(3)
null data sink
BIO_s_secmem(3), BIO_s_mem(3), BIO_set_mem_eof_return(3), BIO_get_mem_data(3), BIO_set_mem_buf(3), BIO_get_mem_ptr(3), BIO_new_mem_buf(3)
memory BIO
BIO_s_socket(3), BIO_new_socket(3)
socket BIO
BIO_set_callback_ex(3), BIO_get_callback_ex(3), BIO_set_callback(3), BIO_get_callback(3), BIO_set_callback_arg(3), BIO_get_callback_arg(3), BIO_debug_callback(3), BIO_callback_fn_ex(3), BIO_callback_fn(3)
BIO callback functions
BIO_set_conn_address(3), BIO_get_conn_address(3), BIO_s_connect(3), BIO_new_connect(3), BIO_set_conn_hostname(3), BIO_set_conn_port(3), BIO_set_conn_ip_family(3), BIO_get_conn_ip_family(3), BIO_get_conn_hostname(3), BIO_get_conn_port(3), BIO_set_nbio(3), BIO_do_connect(3)
connect BIO
BIO_set_data(3), BIO_get_data(3), BIO_set_init(3), BIO_get_init(3), BIO_set_shutdown(3), BIO_get_shutdown(3)
functions for managing BIO state information
BIO_should_read(3), BIO_should_write(3), BIO_should_io_special(3), BIO_retry_type(3), BIO_should_retry(3), BIO_get_retry_BIO(3), BIO_get_retry_reason(3), BIO_set_retry_reason(3)
BIO retry functions
BIO_socket(3), BIO_bind(3), BIO_connect(3), BIO_listen(3), BIO_accept_ex(3), BIO_closesocket(3)
BIO socket communication setup routines
DECLARE_PEM_rw(3), PEM_read_CMS(3), PEM_read_bio_CMS(3), PEM_write_CMS(3), PEM_write_bio_CMS(3), PEM_write_DHxparams(3), PEM_write_bio_DHxparams(3), PEM_read_ECPKParameters(3), PEM_read_bio_ECPKParameters(3), PEM_write_ECPKParameters(3), PEM_write_bio_ECPKParameters(3), PEM_read_ECPrivateKey(3), PEM_write_ECPrivateKey(3), PEM_write_bio_ECPrivateKey(3), PEM_read_EC_PUBKEY(3), PEM_read_bio_EC_PUBKEY(3), PEM_write_EC_PUBKEY(3), PEM_write_bio_EC_PUBKEY(3), PEM_read_NETSCAPE_CERT_SEQUENCE(3), PEM_read_bio_NETSCAPE_CERT_SEQUENCE(3), PEM_write_NETSCAPE_CERT_SEQUENCE(3), PEM_write_bio_NETSCAPE_CERT_SEQUENCE(3), PEM_read_PKCS8(3), PEM_read_bio_PKCS8(3), PEM_write_PKCS8(3), PEM_write_bio_PKCS8(3), PEM_write_PKCS8_PRIV_KEY_INFO(3), PEM_read_bio_PKCS8_PRIV_KEY_INFO(3), PEM_read_PKCS8_PRIV_KEY_INFO(3), PEM_write_bio_PKCS8_PRIV_KEY_INFO(3), PEM_read_SSL_SESSION(3), PEM_read_bio_SSL_SESSION(3), PEM_write_SSL_SESSION(3), PEM_write_bio_SSL_SESSION(3)
PEM object encoding routines
OCSP_sendreq_new(3), OCSP_sendreq_nbio(3), OCSP_REQ_CTX_free(3), OCSP_set_max_response_length(3), OCSP_REQ_CTX_add1_header(3), OCSP_REQ_CTX_set1_req(3), OCSP_sendreq_bio(3), OCSP_REQ_CTX_i2d(3)
OCSP responder query functions
OPENSSL_Applink(3)
glue between OpenSSL BIO and Win32 compiler run-time
OPENSSL_LH_stats(3), OPENSSL_LH_node_stats(3), OPENSSL_LH_node_usage_stats(3), OPENSSL_LH_stats_bio(3), OPENSSL_LH_node_stats_bio(3), OPENSSL_LH_node_usage_stats_bio(3)
LHASH statistics
PEM_bytes_read_bio(3), PEM_bytes_read_bio_secmem(3)
read a PEM-encoded data structure from a BIO
PEM_read_bio_ex(3), PEM_FLAG_SECURE(3), PEM_FLAG_EAY_COMPATIBLE(3), PEM_FLAG_ONLY_B64(3)
read PEM format files with custom processing
PEM_write(3), PEM_write_bio(3), PEM_read(3), PEM_read_bio(3), PEM_do_header(3), PEM_get_EVP_CIPHER_INFO(3)
PEM encoding routines
PEM_write_bio_CMS_stream(3)
output CMS_ContentInfo structure in PEM format
PEM_write_bio_PKCS7_stream(3)
output PKCS7 structure in PEM format
SSL_get_rbio(3), SSL_get_wbio(3)
get BIO linked to an SSL object
SSL_set_bio(3), SSL_set0_rbio(3), SSL_set0_wbio(3)
connect the SSL object with a BIO
X509_PUBKEY_new(3), X509_PUBKEY_free(3), X509_PUBKEY_set(3), X509_PUBKEY_get0(3), X509_PUBKEY_get(3), d2i_PUBKEY(3), i2d_PUBKEY(3), d2i_PUBKEY_bio(3), d2i_PUBKEY_fp(3), i2d_PUBKEY_fp(3), i2d_PUBKEY_bio(3), X509_PUBKEY_set0_param(3), X509_PUBKEY_get0_param(3)
SubjectPublicKeyInfo public key functions
bio(7)
Basic I/O abstraction
d2i_ACCESS_DESCRIPTION(3), d2i_ADMISSIONS(3), d2i_ADMISSION_SYNTAX(3), d2i_ASIdOrRange(3), d2i_ASIdentifierChoice(3), d2i_ASIdentifiers(3), d2i_ASN1_BIT_STRING(3), d2i_ASN1_BMPSTRING(3), d2i_ASN1_ENUMERATED(3), d2i_ASN1_GENERALIZEDTIME(3), d2i_ASN1_GENERALSTRING(3), d2i_ASN1_IA5STRING(3), d2i_ASN1_INTEGER(3), d2i_ASN1_NULL(3), d2i_ASN1_OBJECT(3), d2i_ASN1_OCTET_STRING(3), d2i_ASN1_PRINTABLE(3), d2i_ASN1_PRINTABLESTRING(3), d2i_ASN1_SEQUENCE_ANY(3), d2i_ASN1_SET_ANY(3), d2i_ASN1_T61STRING(3), d2i_ASN1_TIME(3), d2i_ASN1_TYPE(3), d2i_ASN1_UINTEGER(3), d2i_ASN1_UNIVERSALSTRING(3), d2i_ASN1_UTCTIME(3), d2i_ASN1_UTF8STRING(3), d2i_ASN1_VISIBLESTRING(3), d2i_ASRange(3), d2i_AUTHORITY_INFO_ACCESS(3), d2i_AUTHORITY_KEYID(3), d2i_BASIC_CONSTRAINTS(3), d2i_CERTIFICATEPOLICIES(3), d2i_CMS_ContentInfo(3), d2i_CMS_ReceiptRequest(3), d2i_CMS_bio(3), d2i_CRL_DIST_POINTS(3), d2i_DHxparams(3), d2i_DIRECTORYSTRING(3), d2i_DISPLAYTEXT(3), d2i_DIST_POINT(3), d2i_DIST_POINT_NAME(3), d2i_DSAPrivateKey(3), d2i_DSAPrivateKey_bio(3), d2i_DSAPrivateKey_fp(3), d2i_DSAPublicKey(3), d2i_DSA_PUBKEY(3), d2i_DSA_PUBKEY_bio(3), d2i_DSA_PUBKEY_fp(3), d2i_DSA_SIG(3), d2i_DSAparams(3), d2i_ECDSA_SIG(3), d2i_ECPKParameters(3), d2i_ECParameters(3), d2i_ECPrivateKey(3), d2i_ECPrivateKey_bio(3), d2i_ECPrivateKey_fp(3), d2i_EC_PUBKEY(3), d2i_EC_PUBKEY_bio(3), d2i_EC_PUBKEY_fp(3), d2i_EDIPARTYNAME(3), d2i_ESS_CERT_ID(3), d2i_ESS_ISSUER_SERIAL(3), d2i_ESS_SIGNING_CERT(3), d2i_EXTENDED_KEY_USAGE(3), d2i_GENERAL_NAME(3), d2i_GENERAL_NAMES(3), d2i_IPAddressChoice(3), d2i_IPAddressFamily(3), d2i_IPAddressOrRange(3), d2i_IPAddressRange(3), d2i_ISSUING_DIST_POINT(3), d2i_NAMING_AUTHORITY(3), d2i_NETSCAPE_CERT_SEQUENCE(3), d2i_NETSCAPE_SPKAC(3), d2i_NETSCAPE_SPKI(3), d2i_NOTICEREF(3), d2i_OCSP_BASICRESP(3), d2i_OCSP_CERTID(3), d2i_OCSP_CERTSTATUS(3), d2i_OCSP_CRLID(3), d2i_OCSP_ONEREQ(3), d2i_OCSP_REQINFO(3), d2i_OCSP_REQUEST(3), d2i_OCSP_RESPBYTES(3), d2i_OCSP_RESPDATA(3), d2i_OCSP_RESPID(3), d2i_OCSP_RESPONSE(3), d2i_OCSP_REVOKEDINFO(3), d2i_OCSP_SERVICELOC(3), d2i_OCSP_SIGNATURE(3), d2i_OCSP_SINGLERESP(3), d2i_OTHERNAME(3), d2i_PBE2PARAM(3), d2i_PBEPARAM(3), d2i_PBKDF2PARAM(3), d2i_PKCS12(3), d2i_PKCS12_BAGS(3), d2i_PKCS12_MAC_DATA(3), d2i_PKCS12_SAFEBAG(3), d2i_PKCS12_bio(3), d2i_PKCS12_fp(3), d2i_PKCS7(3), d2i_PKCS7_DIGEST(3), d2i_PKCS7_ENCRYPT(3), d2i_PKCS7_ENC_CONTENT(3), d2i_PKCS7_ENVELOPE(3), d2i_PKCS7_ISSUER_AND_SERIAL(3), d2i_PKCS7_RECIP_INFO(3), d2i_PKCS7_SIGNED(3), d2i_PKCS7_SIGNER_INFO(3), d2i_PKCS7_SIGN_ENVELOPE(3), d2i_PKCS7_bio(3), d2i_PKCS7_fp(3), d2i_PKCS8_PRIV_KEY_INFO(3), d2i_PKCS8_PRIV_KEY_INFO_bio(3), d2i_PKCS8_PRIV_KEY_INFO_fp(3), d2i_PKCS8_bio(3), d2i_PKCS8_fp(3), d2i_PKEY_USAGE_PERIOD(3), d2i_POLICYINFO(3), d2i_POLICYQUALINFO(3), d2i_PROFESSION_INFO(3), d2i_PROXY_CERT_INFO_EXTENSION(3), d2i_PROXY_POLICY(3), d2i_RSAPrivateKey(3), d2i_RSAPrivateKey_bio(3), d2i_RSAPrivateKey_fp(3), d2i_RSAPublicKey(3), d2i_RSAPublicKey_bio(3), d2i_RSAPublicKey_fp(3), d2i_RSA_OAEP_PARAMS(3), d2i_RSA_PSS_PARAMS(3), d2i_RSA_PUBKEY(3), d2i_RSA_PUBKEY_bio(3), d2i_RSA_PUBKEY_fp(3), d2i_SCRYPT_PARAMS(3), d2i_SCT_LIST(3), d2i_SXNET(3), d2i_SXNETID(3), d2i_TS_ACCURACY(3), d2i_TS_MSG_IMPRINT(3), d2i_TS_MSG_IMPRINT_bio(3), d2i_TS_MSG_IMPRINT_fp(3), d2i_TS_REQ(3), d2i_TS_REQ_bio(3), d2i_TS_REQ_fp(3), d2i_TS_RESP(3), d2i_TS_RESP_bio(3), d2i_TS_RESP_fp(3), d2i_TS_STATUS_INFO(3), d2i_TS_TST_INFO(3), d2i_TS_TST_INFO_bio(3), d2i_TS_TST_INFO_fp(3), d2i_USERNOTICE(3), d2i_X509(3), d2i_X509_bio(3), d2i_X509_fp(3), d2i_X509_ALGOR(3), d2i_X509_ALGORS(3), d2i_X509_ATTRIBUTE(3), d2i_X509_CERT_AUX(3), d2i_X509_CINF(3), d2i_X509_CRL(3), d2i_X509_CRL_INFO(3), d2i_X509_CRL_bio(3), d2i_X509_CRL_fp(3), d2i_X509_EXTENSION(3), d2i_X509_EXTENSIONS(3), d2i_X509_NAME(3), d2i_X509_NAME_ENTRY(3), d2i_X509_PUBKEY(3), d2i_X509_REQ(3), d2i_X509_REQ_INFO(3), d2i_X509_REQ_bio(3), d2i_X509_REQ_fp(3), d2i_X509_REVOKED(3), d2i_X509_SIG(3), d2i_X509_VAL(3), i2d_ACCESS_DESCRIPTION(3), i2d_ADMISSIONS(3), i2d_ADMISSION_SYNTAX(3), i2d_ASIdOrRange(3), i2d_ASIdentifierChoice(3), i2d_ASIdentifiers(3), i2d_ASN1_BIT_STRING(3), i2d_ASN1_BMPSTRING(3), i2d_ASN1_ENUMERATED(3), i2d_ASN1_GENERALIZEDTIME(3), i2d_ASN1_GENERALSTRING(3), i2d_ASN1_IA5STRING(3), i2d_ASN1_INTEGER(3), i2d_ASN1_NULL(3), i2d_ASN1_OBJECT(3), i2d_ASN1_OCTET_STRING(3), i2d_ASN1_PRINTABLE(3), i2d_ASN1_PRINTABLESTRING(3), i2d_ASN1_SEQUENCE_ANY(3), i2d_ASN1_SET_ANY(3), i2d_ASN1_T61STRING(3), i2d_ASN1_TIME(3), i2d_ASN1_TYPE(3), i2d_ASN1_UNIVERSALSTRING(3), i2d_ASN1_UTCTIME(3), i2d_ASN1_UTF8STRING(3), i2d_ASN1_VISIBLESTRING(3), i2d_ASN1_bio_stream(3), i2d_ASRange(3), i2d_AUTHORITY_INFO_ACCESS(3), i2d_AUTHORITY_KEYID(3), i2d_BASIC_CONSTRAINTS(3), i2d_CERTIFICATEPOLICIES(3), i2d_CMS_ ContentInfo(3), i2d_CMS_ReceiptRequest(3), i2d_CMS_bio(3), i2d_CRL_DIST_POINTS(3), i2d_DHxparams(3), i2d_DIRECTORYSTRING(3), i2d_DISPLAYTEXT(3), i2d_DIST_POINT(3), i2d_DIST_POINT_NAME(3), i2d_DSAPrivateKey(3), i2d_DSAPrivateKey_bio(3), i2d_DSAPrivateKey_fp(3), i2d_DSAPublicKey(3), i2d_DSA_PUBKEY(3), i2d_DSA_PUBKEY_bio(3), i2d_DSA_PUBKEY_fp(3), i2d_DSA_SIG(3), i2d_DSAparams(3), i2d_ECDSA_SIG(3), i2d_ECPKParameters(3), i2d_ECParameters(3), i2d_ECPrivateKey(3), i2d_ECPrivateKey_bio(3), i2d_ECPrivateKey_fp(3), i2d_EC_PUBKEY(3), i2d_EC_PUBKEY_bio(3), i2d_EC_PUBKEY_fp(3), i2d_EDIPARTYNAME(3), i2d_ESS_CERT_ID(3), i2d_ESS_ISSUER_SERIAL(3), i2d_ESS_SIGNING_CERT(3), i2d_EXTENDED_KEY_USAGE(3), i2d_GENERAL_NAME(3), i2d_GENERAL_NAMES(3), i2d_IPAddressChoice(3), i2d_IPAddressFamily(3), i2d_IPAddressOrRange(3), i2d_IPAddressRange(3), i2d_ISSUING_DIST_POINT(3), i2d_NAMING_AUTHORITY(3), i2d_NETSCAPE_CERT_SEQUENCE(3), i2d_NETSCAPE_SPKAC(3), i2d_NETSCAPE_SPKI(3), i2d_NOTICEREF(3), i2d_OCSP_BASICRESP(3), i2d_OCSP_CERTID(3), i2d_OCSP_CERTSTATUS(3), i2d_OCSP_CRLID(3), i2d_OCSP_ONEREQ(3), i2d_OCSP_REQINFO(3), i2d_OCSP_REQUEST(3), i2d_OCSP_RESPBYTES(3), i2d_OCSP_RESPDATA(3), i2d_OCSP_RESPID(3), i2d_OCSP_RESPONSE(3), i2d_OCSP_REVOKEDINFO(3), i2d_OCSP_SERVICELOC(3), i2d_OCSP_SIGNATURE(3), i2d_OCSP_SINGLERESP(3), i2d_OTHERNAME(3), i2d_PBE2PARAM(3), i2d_PBEPARAM(3), i2d_PBKDF2PARAM(3), i2d_PKCS12(3), i2d_PKCS12_BAGS(3), i2d_PKCS12_MAC_DATA(3), i2d_PKCS12_SAFEBAG(3), i2d_PKCS12_bio(3), i2d_PKCS12_fp(3), i2d_PKCS7(3), i2d_PKCS7_DIGEST(3), i2d_PKCS7_ENCRYPT(3), i2d_PKCS7_ENC_CONTENT(3), i2d_PKCS7_ENVELOPE(3), i2d_PKCS7_ISSUER_AND_SERIAL(3), i2d_PKCS7_NDEF(3), i2d_PKCS7_RECIP_INFO(3), i2d_PKCS7_SIGNED(3), i2d_PKCS7_SIGNER_INFO(3), i2d_PKCS7_SIGN_ENVELOPE(3), i2d_PKCS7_bio(3), i2d_PKCS7_fp(3), i2d_PKCS8PrivateKeyInfo_bio(3), i2d_PKCS8PrivateKeyInfo_fp(3), i2d_PKCS8_PRIV_KEY_INFO(3), i2d_PKCS8_PRIV_KEY_INFO_bio(3), i2d_PKCS8_PRIV_KEY_INFO_fp(3), i2d_PKCS8_bio(3), i2d_PKCS8_fp(3), i2d_PKEY_USAGE_PERIOD(3), i2d_POLICYINFO(3), i2d_POLICYQUALINFO(3), i2d_PROFESSION_INFO(3), i2d_PROXY_CERT_INFO_EXTENSION(3), i2d_PROXY_POLICY(3), i2d_RSAPrivateKey(3), i2d_RSAPrivateKey_bio(3), i2d_RSAPrivateKey_fp(3), i2d_RSAPublicKey(3), i2d_RSAPublicKey_bio(3), i2d_RSAPublicKey_fp(3), i2d_RSA_OAEP_PARAMS(3), i2d_RSA_PSS_PARAMS(3), i2d_RSA_PUBKEY(3), i2d_RSA_PUBKEY_bio(3), i2d_RSA_PUBKEY_fp(3), i2d_SCRYPT_PARAMS(3), i2d_SCT_LIST(3), i2d_SXNET(3), i2d_SXNETID(3), i2d_TS_ACCURACY(3), i2d_TS_MSG_IMPRINT(3), i2d_TS_MSG_IMPRINT_bio(3), i2d_TS_MSG_IMPRINT_fp(3), i2d_TS_REQ(3), i2d_TS_REQ_bio(3), i2d_TS_REQ_fp(3), i2d_TS_RESP(3), i2d_TS_RESP_bio(3), i2d_TS_RESP_fp(3), i2d_TS_STATUS_INFO(3), i2d_TS_TST_INFO(3), i2d_TS_TST_INFO_bio(3), i2d_TS_TST_INFO_fp(3), i2d_USERNOTICE(3), i2d_X509(3), i2d_X509_bio(3), i2d_X509_fp(3), i2d_X509_ALGOR(3), i2d_X509_ALGORS(3), i2d_X509_ATTRIBUTE(3), i2d_X509_CERT_AUX(3), i2d_X509_CINF(3), i2d_X509_CRL(3), i2d_X509_CRL_INFO(3), i2d_X509_CRL_bio(3), i2d_X509_CRL_fp(3), i2d_X509_EXTENSION(3), i2d_X509_EXTENSIONS(3), i2d_X509_NAME(3), i2d_X509_NAME_ENTRY(3), i2d_X509_PUBKEY(3), i2d_X509_REQ(3), i2d_X509_REQ_INFO(3), i2d_X509_REQ_bio(3), i2d_X509_REQ_fp(3), i2d_X509_REVOKED(3), i2d_X509_SIG(3), i2d_X509_VAL(3)
convert objects from/to ASN.1/DER representation
d2i_PKCS8PrivateKey_bio(3), d2i_PKCS8PrivateKey_fp(3), i2d_PKCS8PrivateKey_bio(3), i2d_PKCS8PrivateKey_fp(3), i2d_PKCS8PrivateKey_nid_bio(3), i2d_PKCS8PrivateKey_nid_fp(3)
PKCS#8 format private key functions
d2i_PrivateKey(3), d2i_PublicKey(3), d2i_AutoPrivateKey(3), i2d_PrivateKey(3), i2d_PublicKey(3), d2i_PrivateKey_bio(3), d2i_PrivateKey_fp(3)
decode and encode functions for reading and saving EVP_PKEY structures
i2d_CMS_bio_stream(3)
output CMS_ContentInfo structure in BER format
i2d_PKCS7_bio_stream(3)
output PKCS7 structure in BER format
pem_password_cb(3), PEM_read_bio_PrivateKey(3), PEM_read_PrivateKey(3), PEM_write_bio_PrivateKey(3), PEM_write_bio_PrivateKey_traditional(3), PEM_write_PrivateKey(3), PEM_write_bio_PKCS8PrivateKey(3), PEM_write_PKCS8PrivateKey(3), PEM_write_bio_PKCS8PrivateKey_nid(3), PEM_write_PKCS8PrivateKey_nid(3), PEM_read_bio_PUBKEY(3), PEM_read_PUBKEY(3), PEM_write_bio_PUBKEY(3), PEM_write_PUBKEY(3), PEM_read_bio_RSAPrivateKey(3), PEM_read_RSAPrivateKey(3), PEM_write_bio_RSAPrivateKey(3), PEM_write_RSAPrivateKey(3), PEM_read_bio_RSAPublicKey(3), PEM_read_RSAPublicKey(3), PEM_write_bio_RSAPublicKey(3), PEM_write_RSAPublicKey(3), PEM_read_bio_RSA_PUBKEY(3), PEM_read_RSA_PUBKEY(3), PEM_write_bio_RSA_PUBKEY(3), PEM_write_RSA_PUBKEY(3), PEM_read_bio_DSAPrivateKey(3), PEM_read_DSAPrivateKey(3), PEM_write_bio_DSAPrivateKey(3), PEM_write_DSAPrivateKey(3), PEM_read_bio_DSA_PUBKEY(3), PEM_read_DSA_PUBKEY(3), PEM_write_bio_DSA_PUBKEY(3), PEM_write_DSA_PUBKEY(3), PEM_read_bio_Parameters(3), PEM_write_bio_Parameters(3), PEM_read_bio_DSAparams(3), PEM_read_DSAparams(3), PEM_write_bio_DSAparams(3), PEM_write_DSAparams(3), PEM_read_bio_DHparams(3), PEM_read_DHparams(3), PEM_write_bio_DHparams(3), PEM_write_DHparams(3), PEM_read_bio_X509(3), PEM_read_X509(3), PEM_write_bio_X509(3), PEM_write_X509(3), PEM_read_bio_X509_AUX(3), PEM_read_X509_AUX(3), PEM_write_bio_X509_AUX(3), PEM_write_X509_AUX(3), PEM_read_bio_X509_REQ(3), PEM_read_X509_REQ(3), PEM_write_bio_X509_REQ(3), PEM_write_X509_REQ(3), PEM_write_bio_X509_REQ_NEW(3), PEM_write_X509_REQ_NEW(3), PEM_read_bio_X509_CRL(3), PEM_read_X509_CRL(3), PEM_write_bio_X509_CRL(3), PEM_write_X509_CRL(3), PEM_read_bio_PKCS7(3), PEM_read_PKCS7(3), PEM_write_bio_PKCS7(3), PEM_write_PKCS7(3)
PEM routines
ASN1_item_d2i(3), ASN1_item_d2i_bio(3), ASN1_item_d2i_fp(3), d2i_ASN1_TYPE(3), ASN1_item_i2d(3), ASN1_item_i2d_bio(3), ASN1_item_i2d_fp(3), ASN1_item_ndef_i2d(3), i2d_ASN1_TYPE(3), ASN1_item_dup(3), ASN1_item_print(3)
decode and encode ASN.1 objects
ASN1_item_d2i_ex(3ossl), ASN1_item_d2i(3ossl), ASN1_item_d2i_bio_ex(3ossl), ASN1_item_d2i_bio(3ossl), ASN1_item_d2i_fp_ex(3ossl), ASN1_item_d2i_fp(3ossl), ASN1_item_i2d_mem_bio(3ossl)
decode and encode DER-encoded ASN.1 structures
BIO_ADDR(3), BIO_ADDR_new(3), BIO_ADDR_clear(3), BIO_ADDR_free(3), BIO_ADDR_rawmake(3), BIO_ADDR_family(3), BIO_ADDR_rawaddress(3), BIO_ADDR_rawport(3), BIO_ADDR_hostname_string(3), BIO_ADDR_service_string(3), BIO_ADDR_path_string(3)
BIO_ADDR routines
BIO_ADDR(3ossl), BIO_ADDR_new(3ossl), BIO_ADDR_clear(3ossl), BIO_ADDR_free(3ossl), BIO_ADDR_rawmake(3ossl), BIO_ADDR_family(3ossl), BIO_ADDR_rawaddress(3ossl), BIO_ADDR_rawport(3ossl), BIO_ADDR_hostname_string(3ossl), BIO_ADDR_service_string(3ossl), BIO_ADDR_path_string(3ossl)
BIO_ADDR routines
BIO_ctrl(3), BIO_callback_ctrl(3), BIO_ptr_ctrl(3), BIO_int_ctrl(3), BIO_reset(3), BIO_seek(3), BIO_tell(3), BIO_flush(3), BIO_eof(3), BIO_set_close(3), BIO_get_close(3), BIO_pending(3), BIO_wpending(3), BIO_ctrl_pending(3), BIO_ctrl_wpending(3), BIO_get_info_callback(3), BIO_set_info_callback(3), BIO_info_cb(3), BIO_get_ktls_send(3), BIO_get_ktls_recv(3)
BIO control operations
BIO_ctrl(3ossl), BIO_callback_ctrl(3ossl), BIO_ptr_ctrl(3ossl), BIO_int_ctrl(3ossl), BIO_reset(3ossl), BIO_seek(3ossl), BIO_tell(3ossl), BIO_flush(3ossl), BIO_eof(3ossl), BIO_set_close(3ossl), BIO_get_close(3ossl), BIO_pending(3ossl), BIO_wpending(3ossl), BIO_ctrl_pending(3ossl), BIO_ctrl_wpending(3ossl), BIO_get_info_callback(3ossl), BIO_set_info_callback(3ossl), BIO_info_cb(3ossl), BIO_get_ktls_send(3ossl), BIO_get_ktls_recv(3ossl)
BIO control operations
BIO_do_handshake(3), BIO_f_ssl(3), BIO_set_ssl(3), BIO_get_ssl(3), BIO_set_ssl_mode(3), BIO_set_ssl_renegotiate_bytes(3), BIO_get_num_renegotiates(3), BIO_set_ssl_renegotiate_timeout(3), BIO_new_ssl(3), BIO_new_ssl_connect(3), BIO_new_buffer_ssl_connect(3), BIO_ssl_copy_session_id(3), BIO_ssl_shutdown(3)
SSL BIO
BIO_do_handshake(3ossl), BIO_f_ssl(3ossl), BIO_set_ssl(3ossl), BIO_get_ssl(3ossl), BIO_set_ssl_mode(3ossl), BIO_set_ssl_renegotiate_bytes(3ossl), BIO_get_num_renegotiates(3ossl), BIO_set_ssl_renegotiate_timeout(3ossl), BIO_new_ssl(3ossl), BIO_new_ssl_connect(3ossl), BIO_new_buffer_ssl_connect(3ossl), BIO_ssl_copy_session_id(3ossl), BIO_ssl_shutdown(3ossl)
SSL BIO
BIO_dump(3), BIO_dump_indent(3), BIO_dump_fp(3), BIO_dump_indent_fp(3)
hexadecimal printout of arbitrary byte arrays
BIO_f_asn1(3), asn1_ps_func(3), BIO_asn1_set_prefix(3), BIO_asn1_get_prefix(3), BIO_asn1_set_suffix(3), BIO_asn1_get_suffix(3)
BER-encoding filter BIO
BIO_f_base64(3)
base64 BIO filter
BIO_f_base64(3ossl)
base64 BIO filter
BIO_f_cipher(3), BIO_set_cipher(3), BIO_get_cipher_status(3), BIO_get_cipher_ctx(3)
cipher BIO filter
BIO_f_cipher(3ossl), BIO_set_cipher(3ossl), BIO_get_cipher_status(3ossl), BIO_get_cipher_ctx(3ossl)
cipher BIO filter
BIO_f_md(3), BIO_set_md(3), BIO_get_md(3), BIO_get_md_ctx(3)
message digest BIO filter
BIO_f_md(3ossl), BIO_set_md(3ossl), BIO_get_md(3ossl), BIO_get_md_ctx(3ossl)
message digest BIO filter
BIO_f_null(3)
null filter
BIO_f_null(3ossl)
null filter
BIO_f_prefix(3ossl), BIO_set_prefix(3ossl), BIO_set_indent(3ossl), BIO_get_indent(3ossl)
prefix BIO filter
BIO_f_readbuffer(3ossl)
read only buffering BIO that supports BIO_tell() and BIO_seek()
BIO_find_type(3), BIO_next(3), BIO_method_type(3)
BIO chain traversal
BIO_find_type(3ossl), BIO_next(3ossl), BIO_method_type(3ossl)
BIO chain traversal
BIO_get_buffer_num_lines(3), BIO_set_read_buffer_size(3), BIO_set_write_buffer_size(3), BIO_set_buffer_size(3), BIO_set_buffer_read_data(3), BIO_f_buffer(3)
buffering BIO
BIO_get_buffer_num_lines(3ossl), BIO_set_read_buffer_size(3ossl), BIO_set_write_buffer_size(3ossl), BIO_set_buffer_size(3ossl), BIO_set_buffer_read_data(3ossl), BIO_f_buffer(3ossl)
buffering BIO
BIO_get_ex_new_index(3), BIO_set_ex_data(3), BIO_get_ex_data(3), ENGINE_get_ex_new_index(3), ENGINE_set_ex_data(3), ENGINE_get_ex_data(3), UI_get_ex_new_index(3), UI_set_ex_data(3), UI_get_ex_data(3), X509_get_ex_new_index(3), X509_set_ex_data(3), X509_get_ex_data(3), X509_STORE_get_ex_new_index(3), X509_STORE_set_ex_data(3), X509_STORE_get_ex_data(3), X509_STORE_CTX_get_ex_new_index(3), X509_STORE_CTX_set_ex_data(3), X509_STORE_CTX_get_ex_data(3), DH_get_ex_new_index(3), DH_set_ex_data(3), DH_get_ex_data(3), DSA_get_ex_new_index(3), DSA_set_ex_data(3), DSA_get_ex_data(3), ECDH_get_ex_new_index(3), ECDH_set_ex_data(3), ECDH_get_ex_data(3), EC_KEY_get_ex_new_index(3), EC_KEY_set_ex_data(3), EC_KEY_get_ex_data(3), RSA_get_ex_new_index(3), RSA_set_ex_data(3), RSA_get_ex_data(3)
application-specific data
BIO_get_ex_new_index(3ossl), BIO_set_ex_data(3ossl), BIO_get_ex_data(3ossl), BIO_set_app_data(3ossl), BIO_get_app_data(3ossl), DH_get_ex_new_index(3ossl), DH_set_ex_data(3ossl), DH_get_ex_data(3ossl), DSA_get_ex_new_index(3ossl), DSA_set_ex_data(3ossl), DSA_get_ex_data(3ossl), EC_KEY_get_ex_new_index(3ossl), EC_KEY_set_ex_data(3ossl), EC_KEY_get_ex_data(3ossl), ENGINE_get_ex_new_index(3ossl), ENGINE_set_ex_data(3ossl), ENGINE_get_ex_data(3ossl), EVP_PKEY_get_ex_new_index(3ossl), EVP_PKEY_set_ex_data(3ossl), EVP_PKEY_get_ex_data(3ossl), RSA_get_ex_new_index(3ossl), RSA_set_ex_data(3ossl), RSA_get_ex_data(3ossl), RSA_set_app_data(3ossl), RSA_get_app_data(3ossl), SSL_get_ex_new_index(3ossl), SSL_set_ex_data(3ossl), SSL_get_ex_data(3ossl), SSL_set_app_data(3ossl), SSL_get_app_data(3ossl), SSL_CTX_get_ex_new_index(3ossl), SSL_CTX_set_ex_data(3ossl), SSL_CTX_get_ex_data(3ossl), SSL_CTX_set_app_data(3ossl), SSL_CTX_get_app_data(3ossl), SSL_SESSION_get_ex_new_index(3ossl), SSL_SESSION_set_ex_data(3ossl), SSL_SESSION_get_ex_data(3ossl), SSL_SESSION_set_app_data(3ossl), SSL_SESSION_get_app_data(3ossl), UI_get_ex_new_index(3ossl), UI_set_ex_data(3ossl), UI_get_ex_data(3ossl), UI_set_app_data(3ossl), UI_get_app_data(3ossl), X509_STORE_CTX_get_ex_new_index(3ossl), X509_STORE_CTX_set_ex_data(3ossl), X509_STORE_CTX_get_ex_data(3ossl), X509_STORE_CTX_set_app_data(3ossl), X509_STORE_CTX_get_app_data(3ossl), X509_STORE_get_ex_new_index(3ossl), X509_STORE_set_ex_data(3ossl), X509_STORE_get_ex_data(3ossl), X509_get_ex_new_index(3ossl), X509_set_ex_data(3ossl), X509_get_ex_data(3ossl)
application-specific data
BIO_get_new_index(3), BIO_meth_new(3), BIO_meth_free(3), BIO_meth_get_read_ex(3), BIO_meth_set_read_ex(3), BIO_meth_get_write_ex(3), BIO_meth_set_write_ex(3), BIO_meth_get_write(3), BIO_meth_set_write(3), BIO_meth_get_read(3), BIO_meth_set_read(3), BIO_meth_get_puts(3), BIO_meth_set_puts(3), BIO_meth_get_gets(3), BIO_meth_set_gets(3), BIO_meth_get_ctrl(3), BIO_meth_set_ctrl(3), BIO_meth_get_create(3), BIO_meth_set_create(3), BIO_meth_get_destroy(3), BIO_meth_set_destroy(3), BIO_meth_get_callback_ctrl(3), BIO_meth_set_callback_ctrl(3)
Routines to build up BIO methods
BIO_get_new_index(3ossl), BIO_meth_new(3ossl), BIO_meth_free(3ossl), BIO_meth_get_read_ex(3ossl), BIO_meth_set_read_ex(3ossl), BIO_meth_get_write_ex(3ossl), BIO_meth_set_write_ex(3ossl), BIO_meth_get_write(3ossl), BIO_meth_set_write(3ossl), BIO_meth_get_read(3ossl), BIO_meth_set_read(3ossl), BIO_meth_get_puts(3ossl), BIO_meth_set_puts(3ossl), BIO_meth_get_gets(3ossl), BIO_meth_set_gets(3ossl), BIO_meth_get_ctrl(3ossl), BIO_meth_set_ctrl(3ossl), BIO_meth_get_create(3ossl), BIO_meth_set_create(3ossl), BIO_meth_get_destroy(3ossl), BIO_meth_set_destroy(3ossl), BIO_meth_get_callback_ctrl(3ossl), BIO_meth_set_callback_ctrl(3ossl)
Routines to build up BIO methods
BIO_hostserv_priorities(3), BIO_parse_hostserv(3)
utility routines to parse a standard host and service string
BIO_hostserv_priorities(3ossl), BIO_parse_hostserv(3ossl)
utility routines to parse a standard host and service string
BIO_lookup_type(3), BIO_ADDRINFO(3), BIO_ADDRINFO_next(3), BIO_ADDRINFO_free(3), BIO_ADDRINFO_family(3), BIO_ADDRINFO_socktype(3), BIO_ADDRINFO_protocol(3), BIO_ADDRINFO_address(3), BIO_lookup_ex(3), BIO_lookup(3)
BIO_ADDRINFO type and routines
BIO_lookup_type(3ossl), BIO_ADDRINFO(3ossl), BIO_ADDRINFO_next(3ossl), BIO_ADDRINFO_free(3ossl), BIO_ADDRINFO_family(3ossl), BIO_ADDRINFO_socktype(3ossl), BIO_ADDRINFO_protocol(3ossl), BIO_ADDRINFO_address(3ossl), BIO_lookup_ex(3ossl), BIO_lookup(3ossl)
BIO_ADDRINFO type and routines
BIO_new(3), BIO_up_ref(3), BIO_free(3), BIO_vfree(3), BIO_free_all(3)
BIO allocation and freeing functions
BIO_new_CMS(3)
CMS streaming filter BIO
BIO_new_CMS(3ossl)
CMS streaming filter BIO
BIO_new_NDEF(3)
generic constructor for streaming BIO chains
BIO_new_ex(3ossl), BIO_new(3ossl), BIO_up_ref(3ossl), BIO_free(3ossl), BIO_vfree(3ossl), BIO_free_all(3ossl)
BIO allocation and freeing functions
BIO_printf(3), BIO_vprintf(3), BIO_snprintf(3), BIO_vsnprintf(3)
formatted output to a BIO
BIO_printf(3ossl), BIO_vprintf(3ossl), BIO_snprintf(3ossl), BIO_vsnprintf(3ossl)
formatted output to a BIO
BIO_push(3), BIO_pop(3), BIO_set_next(3)
add and remove BIOs from a chain
BIO_push(3ossl), BIO_pop(3ossl), BIO_set_next(3ossl)
add and remove BIOs from a chain
BIO_read_ex(3), BIO_write_ex(3), BIO_read(3), BIO_write(3), BIO_gets(3), BIO_puts(3)
BIO I/O functions
BIO_read_ex(3ossl), BIO_write_ex(3ossl), BIO_read(3ossl), BIO_write(3ossl), BIO_gets(3ossl), BIO_get_line(3ossl), BIO_puts(3ossl)
BIO I/O functions
BIO_s_accept(3), BIO_set_accept_name(3), BIO_set_accept_port(3), BIO_get_accept_name(3), BIO_get_accept_port(3), BIO_new_accept(3), BIO_set_nbio_accept(3), BIO_set_accept_bios(3), BIO_get_peer_name(3), BIO_get_peer_port(3), BIO_get_accept_ip_family(3), BIO_set_accept_ip_family(3), BIO_set_bind_mode(3), BIO_get_bind_mode(3), BIO_do_accept(3)
accept BIO
BIO_s_accept(3ossl), BIO_set_accept_name(3ossl), BIO_set_accept_port(3ossl), BIO_get_accept_name(3ossl), BIO_get_accept_port(3ossl), BIO_new_accept(3ossl), BIO_set_nbio_accept(3ossl), BIO_set_accept_bios(3ossl), BIO_get_peer_name(3ossl), BIO_get_peer_port(3ossl), BIO_get_accept_ip_family(3ossl), BIO_set_accept_ip_family(3ossl), BIO_set_bind_mode(3ossl), BIO_get_bind_mode(3ossl), BIO_do_accept(3ossl)
accept BIO
BIO_s_bio(3), BIO_make_bio_pair(3), BIO_destroy_bio_pair(3), BIO_shutdown_wr(3), BIO_set_write_buf_size(3), BIO_get_write_buf_size(3), BIO_new_bio_pair(3), BIO_get_write_guarantee(3), BIO_ctrl_get_write_guarantee(3), BIO_get_read_request(3), BIO_ctrl_get_read_request(3), BIO_ctrl_reset_read_request(3)
BIO pair BIO
BIO_s_bio(3ossl), BIO_make_bio_pair(3ossl), BIO_destroy_bio_pair(3ossl), BIO_shutdown_wr(3ossl), BIO_set_write_buf_size(3ossl), BIO_get_write_buf_size(3ossl), BIO_new_bio_pair(3ossl), BIO_get_write_guarantee(3ossl), BIO_ctrl_get_write_guarantee(3ossl), BIO_get_read_request(3ossl), BIO_ctrl_get_read_request(3ossl), BIO_ctrl_reset_read_request(3ossl)
BIO pair BIO
BIO_s_connect(3ossl), BIO_new_connect(3ossl), BIO_set_conn_hostname(3ossl), BIO_set_conn_port(3ossl), BIO_set_conn_address(3ossl), BIO_set_conn_ip_family(3ossl), BIO_get_conn_hostname(3ossl), BIO_get_conn_port(3ossl), BIO_get_conn_address(3ossl), BIO_get_conn_ip_family(3ossl), BIO_set_nbio(3ossl), BIO_do_connect(3ossl)
connect BIO
BIO_s_core(3ossl), BIO_new_from_core_bio(3ossl)
OSSL_CORE_BIO functions
BIO_s_fd(3), BIO_set_fd(3), BIO_get_fd(3), BIO_new_fd(3)
file descriptor BIO
BIO_s_fd(3ossl), BIO_set_fd(3ossl), BIO_get_fd(3ossl), BIO_new_fd(3ossl)
file descriptor BIO
BIO_s_file(3), BIO_new_file(3), BIO_new_fp(3), BIO_set_fp(3), BIO_get_fp(3), BIO_read_filename(3), BIO_write_filename(3), BIO_append_filename(3), BIO_rw_filename(3)
FILE bio
BIO_s_file(3ossl), BIO_new_file(3ossl), BIO_new_fp(3ossl), BIO_set_fp(3ossl), BIO_get_fp(3ossl), BIO_read_filename(3ossl), BIO_write_filename(3ossl), BIO_append_filename(3ossl), BIO_rw_filename(3ossl)
FILE bio
BIO_s_null(3)
null data sink
BIO_s_null(3ossl)
null data sink
BIO_s_secmem(3), BIO_s_mem(3), BIO_set_mem_eof_return(3), BIO_get_mem_data(3), BIO_set_mem_buf(3), BIO_get_mem_ptr(3), BIO_new_mem_buf(3)
memory BIO
BIO_s_secmem(3ossl), BIO_s_mem(3ossl), BIO_set_mem_eof_return(3ossl), BIO_get_mem_data(3ossl), BIO_set_mem_buf(3ossl), BIO_get_mem_ptr(3ossl), BIO_new_mem_buf(3ossl)
memory BIO
BIO_s_socket(3), BIO_new_socket(3)
socket BIO
BIO_s_socket(3ossl), BIO_new_socket(3ossl)
socket BIO
BIO_set_callback_ex(3), BIO_get_callback_ex(3), BIO_set_callback(3), BIO_get_callback(3), BIO_set_callback_arg(3), BIO_get_callback_arg(3), BIO_debug_callback(3), BIO_callback_fn_ex(3), BIO_callback_fn(3)
BIO callback functions
BIO_set_callback_ex(3ossl), BIO_get_callback_ex(3ossl), BIO_set_callback(3ossl), BIO_get_callback(3ossl), BIO_set_callback_arg(3ossl), BIO_get_callback_arg(3ossl), BIO_debug_callback(3ossl), BIO_debug_callback_ex(3ossl), BIO_callback_fn_ex(3ossl), BIO_callback_fn(3ossl)
BIO callback functions
BIO_set_conn_address(3), BIO_get_conn_address(3), BIO_s_connect(3), BIO_new_connect(3), BIO_set_conn_hostname(3), BIO_set_conn_port(3), BIO_set_conn_ip_family(3), BIO_get_conn_ip_family(3), BIO_get_conn_hostname(3), BIO_get_conn_port(3), BIO_set_nbio(3), BIO_do_connect(3)
connect BIO
BIO_set_data(3), BIO_get_data(3), BIO_set_init(3), BIO_get_init(3), BIO_set_shutdown(3), BIO_get_shutdown(3)
functions for managing BIO state information
BIO_set_data(3ossl), BIO_get_data(3ossl), BIO_set_init(3ossl), BIO_get_init(3ossl), BIO_set_shutdown(3ossl), BIO_get_shutdown(3ossl)
functions for managing BIO state information
BIO_should_read(3), BIO_should_write(3), BIO_should_io_special(3), BIO_retry_type(3), BIO_should_retry(3), BIO_get_retry_BIO(3), BIO_get_retry_reason(3), BIO_set_retry_reason(3)
BIO retry functions
BIO_should_read(3ossl), BIO_should_write(3ossl), BIO_should_io_special(3ossl), BIO_retry_type(3ossl), BIO_should_retry(3ossl), BIO_get_retry_BIO(3ossl), BIO_get_retry_reason(3ossl), BIO_set_retry_reason(3ossl)
BIO retry functions
BIO_socket(3), BIO_bind(3), BIO_connect(3), BIO_listen(3), BIO_accept_ex(3), BIO_closesocket(3)
BIO socket communication setup routines
BIO_socket(3ossl), BIO_bind(3ossl), BIO_connect(3ossl), BIO_listen(3ossl), BIO_accept_ex(3ossl), BIO_closesocket(3ossl)
BIO socket communication setup routines
BIO_socket_wait(3ossl), BIO_wait(3ossl), BIO_do_connect_retry(3ossl)
BIO connection utility functions
DECLARE_PEM_rw(3), PEM_read_CMS(3), PEM_read_bio_CMS(3), PEM_write_CMS(3), PEM_write_bio_CMS(3), PEM_write_DHxparams(3), PEM_write_bio_DHxparams(3), PEM_read_ECPKParameters(3), PEM_read_bio_ECPKParameters(3), PEM_write_ECPKParameters(3), PEM_write_bio_ECPKParameters(3), PEM_read_ECPrivateKey(3), PEM_write_ECPrivateKey(3), PEM_write_bio_ECPrivateKey(3), PEM_read_EC_PUBKEY(3), PEM_read_bio_EC_PUBKEY(3), PEM_write_EC_PUBKEY(3), PEM_write_bio_EC_PUBKEY(3), PEM_read_NETSCAPE_CERT_SEQUENCE(3), PEM_read_bio_NETSCAPE_CERT_SEQUENCE(3), PEM_write_NETSCAPE_CERT_SEQUENCE(3), PEM_write_bio_NETSCAPE_CERT_SEQUENCE(3), PEM_read_PKCS8(3), PEM_read_bio_PKCS8(3), PEM_write_PKCS8(3), PEM_write_bio_PKCS8(3), PEM_write_PKCS8_PRIV_KEY_INFO(3), PEM_read_bio_PKCS8_PRIV_KEY_INFO(3), PEM_read_PKCS8_PRIV_KEY_INFO(3), PEM_write_bio_PKCS8_PRIV_KEY_INFO(3), PEM_read_SSL_SESSION(3), PEM_read_bio_SSL_SESSION(3), PEM_write_SSL_SESSION(3), PEM_write_bio_SSL_SESSION(3)
PEM object encoding routines
DECLARE_PEM_rw(3ossl), PEM_read_CMS(3ossl), PEM_read_bio_CMS(3ossl), PEM_write_CMS(3ossl), PEM_write_bio_CMS(3ossl), PEM_write_DHxparams(3ossl), PEM_write_bio_DHxparams(3ossl), PEM_read_ECPKParameters(3ossl), PEM_read_bio_ECPKParameters(3ossl), PEM_write_ECPKParameters(3ossl), PEM_write_bio_ECPKParameters(3ossl), PEM_read_ECPrivateKey(3ossl), PEM_write_ECPrivateKey(3ossl), PEM_write_bio_ECPrivateKey(3ossl), PEM_read_EC_PUBKEY(3ossl), PEM_read_bio_EC_PUBKEY(3ossl), PEM_write_EC_PUBKEY(3ossl), PEM_write_bio_EC_PUBKEY(3ossl), PEM_read_NETSCAPE_CERT_SEQUENCE(3ossl), PEM_read_bio_NETSCAPE_CERT_SEQUENCE(3ossl), PEM_write_NETSCAPE_CERT_SEQUENCE(3ossl), PEM_write_bio_NETSCAPE_CERT_SEQUENCE(3ossl), PEM_read_PKCS8(3ossl), PEM_read_bio_PKCS8(3ossl), PEM_write_PKCS8(3ossl), PEM_write_bio_PKCS8(3ossl), PEM_write_PKCS8_PRIV_KEY_INFO(3ossl), PEM_read_bio_PKCS8_PRIV_KEY_INFO(3ossl), PEM_read_PKCS8_PRIV_KEY_INFO(3ossl), PEM_write_bio_PKCS8_PRIV_KEY_INFO(3ossl), PEM_read_SSL_SESSION(3ossl), PEM_read_bio_SSL_SESSION(3ossl), PEM_write_SSL_SESSION(3ossl), PEM_write_bio_SSL_SESSION(3ossl), PEM_read_X509_PUBKEY(3ossl), PEM_read_bio_X509_PUBKEY(3ossl), PEM_write_X509_PUBKEY(3ossl), PEM_write_bio_X509_PUBKEY(3ossl)
PEM object encoding routines
ERR_raise(3ossl), ERR_raise_data(3ossl), ERR_put_error(3ossl), ERR_add_error_data(3ossl), ERR_add_error_vdata(3ossl), ERR_add_error_txt(3ossl), ERR_add_error_mem_bio(3ossl)
record an error
OCSP_REQ_CTX(3ossl), OCSP_sendreq_new(3ossl), OCSP_sendreq_nbio(3ossl), OCSP_sendreq_bio(3ossl), OCSP_REQ_CTX_i2d(3ossl), OCSP_REQ_CTX_add1_header(3ossl), OCSP_REQ_CTX_free(3ossl), OCSP_set_max_response_length(3ossl), OCSP_REQ_CTX_set1_req(3ossl)
OCSP responder query functions
OCSP_sendreq_new(3), OCSP_sendreq_nbio(3), OCSP_REQ_CTX_free(3), OCSP_set_max_response_length(3), OCSP_REQ_CTX_add1_header(3), OCSP_REQ_CTX_set1_req(3), OCSP_sendreq_bio(3), OCSP_REQ_CTX_i2d(3)
OCSP responder query functions
OPENSSL_Applink(3)
glue between OpenSSL BIO and Win32 compiler run-time
OPENSSL_Applink(3ossl)
glue between OpenSSL BIO and Win32 compiler run-time
OPENSSL_LH_stats(3), OPENSSL_LH_node_stats(3), OPENSSL_LH_node_usage_stats(3), OPENSSL_LH_stats_bio(3), OPENSSL_LH_node_stats_bio(3), OPENSSL_LH_node_usage_stats_bio(3)
LHASH statistics
OPENSSL_LH_stats(3ossl), OPENSSL_LH_node_stats(3ossl), OPENSSL_LH_node_usage_stats(3ossl), OPENSSL_LH_stats_bio(3ossl), OPENSSL_LH_node_stats_bio(3ossl), OPENSSL_LH_node_usage_stats_bio(3ossl)
LHASH statistics
OSSL_CMP_MSG_get0_header(3ossl), OSSL_CMP_MSG_get_bodytype(3ossl), OSSL_CMP_MSG_update_transactionID(3ossl), OSSL_CMP_CTX_setup_CRM(3ossl), OSSL_CMP_MSG_read(3ossl), OSSL_CMP_MSG_write(3ossl), d2i_OSSL_CMP_MSG_bio(3ossl), i2d_OSSL_CMP_MSG_bio(3ossl)
function(s) manipulating CMP messages
OSSL_CMP_log_open(3ossl), OSSL_CMP_log_close(3ossl), OSSL_CMP_severity(3ossl), OSSL_CMP_LOG_EMERG(3ossl), OSSL_CMP_LOG_ALERT(3ossl), OSSL_CMP_LOG_CRIT(3ossl), OSSL_CMP_LOG_ERR(3ossl), OSSL_CMP_LOG_WARNING(3ossl), OSSL_CMP_LOG_NOTICE(3ossl), OSSL_CMP_LOG_INFO(3ossl), OSSL_CMP_LOG_DEBUG(3ossl), OSSL_CMP_LOG_TRACE(3ossl), OSSL_CMP_log_cb_t(3ossl), OSSL_CMP_print_to_bio(3ossl), OSSL_CMP_print_errors_cb(3ossl)
functions for logging and error reporting
OSSL_DECODER_from_data(3ossl), OSSL_DECODER_from_bio(3ossl), OSSL_DECODER_from_fp(3ossl)
Routines to perform a decoding
OSSL_ENCODER_to_data(3ossl), OSSL_ENCODER_to_bio(3ossl), OSSL_ENCODER_to_fp(3ossl)
Routines to perform an encoding
OSSL_HTTP_REQ_CTX(3ossl), OSSL_HTTP_REQ_CTX_new(3ossl), OSSL_HTTP_REQ_CTX_free(3ossl), OSSL_HTTP_REQ_CTX_set_request_line(3ossl), OSSL_HTTP_REQ_CTX_add1_header(3ossl), OSSL_HTTP_REQ_CTX_set_expected(3ossl), OSSL_HTTP_REQ_CTX_set1_req(3ossl), OSSL_HTTP_REQ_CTX_nbio(3ossl), OSSL_HTTP_REQ_CTX_nbio_d2i(3ossl), OSSL_HTTP_REQ_CTX_exchange(3ossl), OSSL_HTTP_REQ_CTX_get0_mem_bio(3ossl), OSSL_HTTP_REQ_CTX_get_resp_len(3ossl), OSSL_HTTP_REQ_CTX_set_max_response_length(3ossl), OSSL_HTTP_is_alive(3ossl)
HTTP client low-level functions
OSSL_HTTP_open(3ossl), OSSL_HTTP_bio_cb_t(3ossl), OSSL_HTTP_proxy_connect(3ossl), OSSL_HTTP_set1_request(3ossl), OSSL_HTTP_exchange(3ossl), OSSL_HTTP_get(3ossl), OSSL_HTTP_transfer(3ossl), OSSL_HTTP_close(3ossl)
HTTP client high-level functions
OSSL_STORE_attach(3ossl)
Functions to read objects from a BIO
PEM_X509_INFO_read(3), PEM_X509_INFO_read_bio(3)
PEM and DER decode X.509 certificates, private keys, and revocation lists
PEM_X509_INFO_read_bio_ex(3ossl), PEM_X509_INFO_read_ex(3ossl)
read PEM-encoded data structures into one or more X509_INFO objects
PEM_bytes_read_bio(3), PEM_bytes_read_bio_secmem(3)
read a PEM-encoded data structure from a BIO
PEM_bytes_read_bio(3ossl), PEM_bytes_read_bio_secmem(3ossl)
read a PEM-encoded data structure from a BIO
PEM_read_bio_ex(3), PEM_FLAG_SECURE(3), PEM_FLAG_EAY_COMPATIBLE(3), PEM_FLAG_ONLY_B64(3)
read PEM format files with custom processing
PEM_read_bio_ex(3ossl), PEM_FLAG_SECURE(3ossl), PEM_FLAG_EAY_COMPATIBLE(3ossl), PEM_FLAG_ONLY_B64(3ossl)
read PEM format files with custom processing
PEM_write(3), PEM_write_bio(3), PEM_read(3), PEM_read_bio(3), PEM_do_header(3), PEM_get_EVP_CIPHER_INFO(3)
PEM encoding routines
PEM_write(3ossl), PEM_write_bio(3ossl), PEM_read(3ossl), PEM_read_bio(3ossl), PEM_do_header(3ossl), PEM_get_EVP_CIPHER_INFO(3ossl)
PEM encoding routines
PEM_write_bio_ASN1_stream(3)
generic PEM encoder
PEM_write_bio_CMS_stream(3)
output CMS_ContentInfo structure in PEM format
PEM_write_bio_CMS_stream(3ossl)
output CMS_ContentInfo structure in PEM format
PEM_write_bio_PKCS7_stream(3)
output PKCS7 structure in PEM format
PEM_write_bio_PKCS7_stream(3ossl)
output PKCS7 structure in PEM format
PKCS7_dataFinal(3)
move data from a BIO chain to a ContentInfo object
PKCS7_dataInit(3)
construct a BIO chain for adding or retrieving content
PKCS7_final(3)
read data from a BIO into a ContentInfo object
SMIME_crlf_copy(3)
buffered copy between BIOs
SSL_get_rbio(3), SSL_get_wbio(3)
get BIO linked to an SSL object
SSL_get_rbio(3ossl), SSL_get_wbio(3ossl)
get BIO linked to an SSL object
SSL_set_bio(3), SSL_set0_rbio(3), SSL_set0_wbio(3)
connect the SSL object with a BIO
SSL_set_bio(3ossl), SSL_set0_rbio(3ossl), SSL_set0_wbio(3ossl)
connect the SSL object with a BIO
X509_PUBKEY_new(3), X509_PUBKEY_free(3), X509_PUBKEY_set(3), X509_PUBKEY_get0(3), X509_PUBKEY_get(3), d2i_PUBKEY(3), i2d_PUBKEY(3), d2i_PUBKEY_bio(3), d2i_PUBKEY_fp(3), i2d_PUBKEY_fp(3), i2d_PUBKEY_bio(3), X509_PUBKEY_set0_param(3), X509_PUBKEY_get0_param(3)
SubjectPublicKeyInfo public key functions
X509_PUBKEY_new_ex(3ossl), X509_PUBKEY_new(3ossl), X509_PUBKEY_free(3ossl), X509_PUBKEY_dup(3ossl), X509_PUBKEY_set(3ossl), X509_PUBKEY_get0(3ossl), X509_PUBKEY_get(3ossl), d2i_PUBKEY_ex(3ossl), d2i_PUBKEY(3ossl), i2d_PUBKEY(3ossl), d2i_PUBKEY_bio(3ossl), d2i_PUBKEY_fp(3ossl), i2d_PUBKEY_fp(3ossl), i2d_PUBKEY_bio(3ossl), X509_PUBKEY_set0_param(3ossl), X509_PUBKEY_get0_param(3ossl), X509_PUBKEY_eq(3ossl)
SubjectPublicKeyInfo public key functions
X509_load_http(3ossl), X509_http_nbio(3ossl), X509_CRL_load_http(3ossl), X509_CRL_http_nbio(3ossl)
certificate and CRL loading functions
asn2all(1)
generate reports from ASN.1 biological data
asn2ff(1)
convert ASN.1 biological data to a flat format (old version)
asn2fsa(1)
convert biological sequence data from ASN.1 to FASTA
asn2gb(1)
convert ASN.1 biological data to a GenBank-style flat format
asn2idx(1)
index ASN.1 Bioseq-sets for fast access to individual sequences
asn2xml(1)
translate biological data from ASN.1 to XML
asndisc(1)
check ASN.1 biological sequence records for discrepancies
asnmacro(1)
process ASN.1 biological data per Sequin macros
asnval(1)
validate ASN.1 biological sequence records
aubio(1)
a command line tool to extract information from sound files
aubiocut(1)
a command line tool to slice sound files at onset or beat timestamps
aubiomfcc(1)
a command line tool to compute Mel-Frequency Cepstrum Coefficients
aubionotes(1)
a command line tool to extract musical notes
aubioonset(1)
a command line tool to extract musical onset times
aubiopitch(1)
a command line tool to extract musical pitch
aubioquiet(1)
a command line tool to extracts quiet and loud regions from a file
aubiotrack(1)
a command line tool to extract musical beats from audio signals
b2i_PVK_bio(3ossl), b2i_PVK_bio_ex(3ossl), i2b_PVK_bio(3ossl), i2b_PVK_bio_ex(3ossl)
Decode and encode functions for reading and writing MSBLOB format private keys
bin2rec(1)
converts biosignal data produced with rec2bin, into a gdf file. rec2bin and bin2rec are complementary functions, which can be useful to dump data, edit date and revert it back into the original format
bio(7)
Basic I/O abstraction
bio(7ossl)
Basic I/O abstraction
biof(1)
rotating stack of quads
biolibc(3), BIOLIBC(3)
Library of high-performance low-level functions for bioinformatics programming
bioradtopgm(1)
convert a Biorad confocal file into a PGM image synopsis
biorythm(6)
simple biorythm calculation program
biosfont(4)
retrieve font bitmaps from BIOS memory
biosig2gdf(1)
converts different biomedical signal file formats into a simplified version of GDF, and can stream the result to stdout. This is useful for reading the data by an unnamed pipe into different programming environment, while a simplified parser can be used to decode the data. The conversion performs a conversion to GDFv3 format, where all channels have the same data type and the same sampling rate
biosig_fhir(1)
provides fhir binary template for biosignal data
bugsx(1)
display and evolve biomorphs
d2i_ACCESS_DESCRIPTION(3), d2i_ADMISSIONS(3), d2i_ADMISSION_SYNTAX(3), d2i_ASIdOrRange(3), d2i_ASIdentifierChoice(3), d2i_ASIdentifiers(3), d2i_ASN1_BIT_STRING(3), d2i_ASN1_BMPSTRING(3), d2i_ASN1_ENUMERATED(3), d2i_ASN1_GENERALIZEDTIME(3), d2i_ASN1_GENERALSTRING(3), d2i_ASN1_IA5STRING(3), d2i_ASN1_INTEGER(3), d2i_ASN1_NULL(3), d2i_ASN1_OBJECT(3), d2i_ASN1_OCTET_STRING(3), d2i_ASN1_PRINTABLE(3), d2i_ASN1_PRINTABLESTRING(3), d2i_ASN1_SEQUENCE_ANY(3), d2i_ASN1_SET_ANY(3), d2i_ASN1_T61STRING(3), d2i_ASN1_TIME(3), d2i_ASN1_TYPE(3), d2i_ASN1_UINTEGER(3), d2i_ASN1_UNIVERSALSTRING(3), d2i_ASN1_UTCTIME(3), d2i_ASN1_UTF8STRING(3), d2i_ASN1_VISIBLESTRING(3), d2i_ASRange(3), d2i_AUTHORITY_INFO_ACCESS(3), d2i_AUTHORITY_KEYID(3), d2i_BASIC_CONSTRAINTS(3), d2i_CERTIFICATEPOLICIES(3), d2i_CMS_ContentInfo(3), d2i_CMS_ReceiptRequest(3), d2i_CMS_bio(3), d2i_CRL_DIST_POINTS(3), d2i_DHxparams(3), d2i_DIRECTORYSTRING(3), d2i_DISPLAYTEXT(3), d2i_DIST_POINT(3), d2i_DIST_POINT_NAME(3), d2i_DSAPrivateKey(3), d2i_DSAPrivateKey_bio(3), d2i_DSAPrivateKey_fp(3), d2i_DSAPublicKey(3), d2i_DSA_PUBKEY(3), d2i_DSA_PUBKEY_bio(3), d2i_DSA_PUBKEY_fp(3), d2i_DSA_SIG(3), d2i_DSAparams(3), d2i_ECDSA_SIG(3), d2i_ECPKParameters(3), d2i_ECParameters(3), d2i_ECPrivateKey(3), d2i_ECPrivateKey_bio(3), d2i_ECPrivateKey_fp(3), d2i_EC_PUBKEY(3), d2i_EC_PUBKEY_bio(3), d2i_EC_PUBKEY_fp(3), d2i_EDIPARTYNAME(3), d2i_ESS_CERT_ID(3), d2i_ESS_ISSUER_SERIAL(3), d2i_ESS_SIGNING_CERT(3), d2i_EXTENDED_KEY_USAGE(3), d2i_GENERAL_NAME(3), d2i_GENERAL_NAMES(3), d2i_IPAddressChoice(3), d2i_IPAddressFamily(3), d2i_IPAddressOrRange(3), d2i_IPAddressRange(3), d2i_ISSUING_DIST_POINT(3), d2i_NAMING_AUTHORITY(3), d2i_NETSCAPE_CERT_SEQUENCE(3), d2i_NETSCAPE_SPKAC(3), d2i_NETSCAPE_SPKI(3), d2i_NOTICEREF(3), d2i_OCSP_BASICRESP(3), d2i_OCSP_CERTID(3), d2i_OCSP_CERTSTATUS(3), d2i_OCSP_CRLID(3), d2i_OCSP_ONEREQ(3), d2i_OCSP_REQINFO(3), d2i_OCSP_REQUEST(3), d2i_OCSP_RESPBYTES(3), d2i_OCSP_RESPDATA(3), d2i_OCSP_RESPID(3), d2i_OCSP_RESPONSE(3), d2i_OCSP_REVOKEDINFO(3), d2i_OCSP_SERVICELOC(3), d2i_OCSP_SIGNATURE(3), d2i_OCSP_SINGLERESP(3), d2i_OTHERNAME(3), d2i_PBE2PARAM(3), d2i_PBEPARAM(3), d2i_PBKDF2PARAM(3), d2i_PKCS12(3), d2i_PKCS12_BAGS(3), d2i_PKCS12_MAC_DATA(3), d2i_PKCS12_SAFEBAG(3), d2i_PKCS12_bio(3), d2i_PKCS12_fp(3), d2i_PKCS7(3), d2i_PKCS7_DIGEST(3), d2i_PKCS7_ENCRYPT(3), d2i_PKCS7_ENC_CONTENT(3), d2i_PKCS7_ENVELOPE(3), d2i_PKCS7_ISSUER_AND_SERIAL(3), d2i_PKCS7_RECIP_INFO(3), d2i_PKCS7_SIGNED(3), d2i_PKCS7_SIGNER_INFO(3), d2i_PKCS7_SIGN_ENVELOPE(3), d2i_PKCS7_bio(3), d2i_PKCS7_fp(3), d2i_PKCS8_PRIV_KEY_INFO(3), d2i_PKCS8_PRIV_KEY_INFO_bio(3), d2i_PKCS8_PRIV_KEY_INFO_fp(3), d2i_PKCS8_bio(3), d2i_PKCS8_fp(3), d2i_PKEY_USAGE_PERIOD(3), d2i_POLICYINFO(3), d2i_POLICYQUALINFO(3), d2i_PROFESSION_INFO(3), d2i_PROXY_CERT_INFO_EXTENSION(3), d2i_PROXY_POLICY(3), d2i_RSAPrivateKey(3), d2i_RSAPrivateKey_bio(3), d2i_RSAPrivateKey_fp(3), d2i_RSAPublicKey(3), d2i_RSAPublicKey_bio(3), d2i_RSAPublicKey_fp(3), d2i_RSA_OAEP_PARAMS(3), d2i_RSA_PSS_PARAMS(3), d2i_RSA_PUBKEY(3), d2i_RSA_PUBKEY_bio(3), d2i_RSA_PUBKEY_fp(3), d2i_SCRYPT_PARAMS(3), d2i_SCT_LIST(3), d2i_SXNET(3), d2i_SXNETID(3), d2i_TS_ACCURACY(3), d2i_TS_MSG_IMPRINT(3), d2i_TS_MSG_IMPRINT_bio(3), d2i_TS_MSG_IMPRINT_fp(3), d2i_TS_REQ(3), d2i_TS_REQ_bio(3), d2i_TS_REQ_fp(3), d2i_TS_RESP(3), d2i_TS_RESP_bio(3), d2i_TS_RESP_fp(3), d2i_TS_STATUS_INFO(3), d2i_TS_TST_INFO(3), d2i_TS_TST_INFO_bio(3), d2i_TS_TST_INFO_fp(3), d2i_USERNOTICE(3), d2i_X509(3), d2i_X509_bio(3), d2i_X509_fp(3), d2i_X509_ALGOR(3), d2i_X509_ALGORS(3), d2i_X509_ATTRIBUTE(3), d2i_X509_CERT_AUX(3), d2i_X509_CINF(3), d2i_X509_CRL(3), d2i_X509_CRL_INFO(3), d2i_X509_CRL_bio(3), d2i_X509_CRL_fp(3), d2i_X509_EXTENSION(3), d2i_X509_EXTENSIONS(3), d2i_X509_NAME(3), d2i_X509_NAME_ENTRY(3), d2i_X509_PUBKEY(3), d2i_X509_REQ(3), d2i_X509_REQ_INFO(3), d2i_X509_REQ_bio(3), d2i_X509_REQ_fp(3), d2i_X509_REVOKED(3), d2i_X509_SIG(3), d2i_X509_VAL(3), i2d_ACCESS_DESCRIPTION(3), i2d_ADMISSIONS(3), i2d_ADMISSION_SYNTAX(3), i2d_ASIdOrRange(3), i2d_ASIdentifierChoice(3), i2d_ASIdentifiers(3), i2d_ASN1_BIT_STRING(3), i2d_ASN1_BMPSTRING(3), i2d_ASN1_ENUMERATED(3), i2d_ASN1_GENERALIZEDTIME(3), i2d_ASN1_GENERALSTRING(3), i2d_ASN1_IA5STRING(3), i2d_ASN1_INTEGER(3), i2d_ASN1_NULL(3), i2d_ASN1_OBJECT(3), i2d_ASN1_OCTET_STRING(3), i2d_ASN1_PRINTABLE(3), i2d_ASN1_PRINTABLESTRING(3), i2d_ASN1_SEQUENCE_ANY(3), i2d_ASN1_SET_ANY(3), i2d_ASN1_T61STRING(3), i2d_ASN1_TIME(3), i2d_ASN1_TYPE(3), i2d_ASN1_UNIVERSALSTRING(3), i2d_ASN1_UTCTIME(3), i2d_ASN1_UTF8STRING(3), i2d_ASN1_VISIBLESTRING(3), i2d_ASN1_bio_stream(3), i2d_ASRange(3), i2d_AUTHORITY_INFO_ACCESS(3), i2d_AUTHORITY_KEYID(3), i2d_BASIC_CONSTRAINTS(3), i2d_CERTIFICATEPOLICIES(3), i2d_CMS_ ContentInfo(3), i2d_CMS_ReceiptRequest(3), i2d_CMS_bio(3), i2d_CRL_DIST_POINTS(3), i2d_DHxparams(3), i2d_DIRECTORYSTRING(3), i2d_DISPLAYTEXT(3), i2d_DIST_POINT(3), i2d_DIST_POINT_NAME(3), i2d_DSAPrivateKey(3), i2d_DSAPrivateKey_bio(3), i2d_DSAPrivateKey_fp(3), i2d_DSAPublicKey(3), i2d_DSA_PUBKEY(3), i2d_DSA_PUBKEY_bio(3), i2d_DSA_PUBKEY_fp(3), i2d_DSA_SIG(3), i2d_DSAparams(3), i2d_ECDSA_SIG(3), i2d_ECPKParameters(3), i2d_ECParameters(3), i2d_ECPrivateKey(3), i2d_ECPrivateKey_bio(3), i2d_ECPrivateKey_fp(3), i2d_EC_PUBKEY(3), i2d_EC_PUBKEY_bio(3), i2d_EC_PUBKEY_fp(3), i2d_EDIPARTYNAME(3), i2d_ESS_CERT_ID(3), i2d_ESS_ISSUER_SERIAL(3), i2d_ESS_SIGNING_CERT(3), i2d_EXTENDED_KEY_USAGE(3), i2d_GENERAL_NAME(3), i2d_GENERAL_NAMES(3), i2d_IPAddressChoice(3), i2d_IPAddressFamily(3), i2d_IPAddressOrRange(3), i2d_IPAddressRange(3), i2d_ISSUING_DIST_POINT(3), i2d_NAMING_AUTHORITY(3), i2d_NETSCAPE_CERT_SEQUENCE(3), i2d_NETSCAPE_SPKAC(3), i2d_NETSCAPE_SPKI(3), i2d_NOTICEREF(3), i2d_OCSP_BASICRESP(3), i2d_OCSP_CERTID(3), i2d_OCSP_CERTSTATUS(3), i2d_OCSP_CRLID(3), i2d_OCSP_ONEREQ(3), i2d_OCSP_REQINFO(3), i2d_OCSP_REQUEST(3), i2d_OCSP_RESPBYTES(3), i2d_OCSP_RESPDATA(3), i2d_OCSP_RESPID(3), i2d_OCSP_RESPONSE(3), i2d_OCSP_REVOKEDINFO(3), i2d_OCSP_SERVICELOC(3), i2d_OCSP_SIGNATURE(3), i2d_OCSP_SINGLERESP(3), i2d_OTHERNAME(3), i2d_PBE2PARAM(3), i2d_PBEPARAM(3), i2d_PBKDF2PARAM(3), i2d_PKCS12(3), i2d_PKCS12_BAGS(3), i2d_PKCS12_MAC_DATA(3), i2d_PKCS12_SAFEBAG(3), i2d_PKCS12_bio(3), i2d_PKCS12_fp(3), i2d_PKCS7(3), i2d_PKCS7_DIGEST(3), i2d_PKCS7_ENCRYPT(3), i2d_PKCS7_ENC_CONTENT(3), i2d_PKCS7_ENVELOPE(3), i2d_PKCS7_ISSUER_AND_SERIAL(3), i2d_PKCS7_NDEF(3), i2d_PKCS7_RECIP_INFO(3), i2d_PKCS7_SIGNED(3), i2d_PKCS7_SIGNER_INFO(3), i2d_PKCS7_SIGN_ENVELOPE(3), i2d_PKCS7_bio(3), i2d_PKCS7_fp(3), i2d_PKCS8PrivateKeyInfo_bio(3), i2d_PKCS8PrivateKeyInfo_fp(3), i2d_PKCS8_PRIV_KEY_INFO(3), i2d_PKCS8_PRIV_KEY_INFO_bio(3), i2d_PKCS8_PRIV_KEY_INFO_fp(3), i2d_PKCS8_bio(3), i2d_PKCS8_fp(3), i2d_PKEY_USAGE_PERIOD(3), i2d_POLICYINFO(3), i2d_POLICYQUALINFO(3), i2d_PROFESSION_INFO(3), i2d_PROXY_CERT_INFO_EXTENSION(3), i2d_PROXY_POLICY(3), i2d_RSAPrivateKey(3), i2d_RSAPrivateKey_bio(3), i2d_RSAPrivateKey_fp(3), i2d_RSAPublicKey(3), i2d_RSAPublicKey_bio(3), i2d_RSAPublicKey_fp(3), i2d_RSA_OAEP_PARAMS(3), i2d_RSA_PSS_PARAMS(3), i2d_RSA_PUBKEY(3), i2d_RSA_PUBKEY_bio(3), i2d_RSA_PUBKEY_fp(3), i2d_SCRYPT_PARAMS(3), i2d_SCT_LIST(3), i2d_SXNET(3), i2d_SXNETID(3), i2d_TS_ACCURACY(3), i2d_TS_MSG_IMPRINT(3), i2d_TS_MSG_IMPRINT_bio(3), i2d_TS_MSG_IMPRINT_fp(3), i2d_TS_REQ(3), i2d_TS_REQ_bio(3), i2d_TS_REQ_fp(3), i2d_TS_RESP(3), i2d_TS_RESP_bio(3), i2d_TS_RESP_fp(3), i2d_TS_STATUS_INFO(3), i2d_TS_TST_INFO(3), i2d_TS_TST_INFO_bio(3), i2d_TS_TST_INFO_fp(3), i2d_USERNOTICE(3), i2d_X509(3), i2d_X509_bio(3), i2d_X509_fp(3), i2d_X509_ALGOR(3), i2d_X509_ALGORS(3), i2d_X509_ATTRIBUTE(3), i2d_X509_CERT_AUX(3), i2d_X509_CINF(3), i2d_X509_CRL(3), i2d_X509_CRL_INFO(3), i2d_X509_CRL_bio(3), i2d_X509_CRL_fp(3), i2d_X509_EXTENSION(3), i2d_X509_EXTENSIONS(3), i2d_X509_NAME(3), i2d_X509_NAME_ENTRY(3), i2d_X509_PUBKEY(3), i2d_X509_REQ(3), i2d_X509_REQ_INFO(3), i2d_X509_REQ_bio(3), i2d_X509_REQ_fp(3), i2d_X509_REVOKED(3), i2d_X509_SIG(3), i2d_X509_VAL(3)
convert objects from/to ASN.1/DER representation
d2i_ACCESS_DESCRIPTION(3ossl), d2i_ADMISSIONS(3ossl), d2i_ADMISSION_SYNTAX(3ossl), d2i_ASIdOrRange(3ossl), d2i_ASIdentifierChoice(3ossl), d2i_ASIdentifiers(3ossl), d2i_ASN1_BIT_STRING(3ossl), d2i_ASN1_BMPSTRING(3ossl), d2i_ASN1_ENUMERATED(3ossl), d2i_ASN1_GENERALIZEDTIME(3ossl), d2i_ASN1_GENERALSTRING(3ossl), d2i_ASN1_IA5STRING(3ossl), d2i_ASN1_INTEGER(3ossl), d2i_ASN1_NULL(3ossl), d2i_ASN1_OBJECT(3ossl), d2i_ASN1_OCTET_STRING(3ossl), d2i_ASN1_PRINTABLE(3ossl), d2i_ASN1_PRINTABLESTRING(3ossl), d2i_ASN1_SEQUENCE_ANY(3ossl), d2i_ASN1_SET_ANY(3ossl), d2i_ASN1_T61STRING(3ossl), d2i_ASN1_TIME(3ossl), d2i_ASN1_TYPE(3ossl), d2i_ASN1_UINTEGER(3ossl), d2i_ASN1_UNIVERSALSTRING(3ossl), d2i_ASN1_UTCTIME(3ossl), d2i_ASN1_UTF8STRING(3ossl), d2i_ASN1_VISIBLESTRING(3ossl), d2i_ASRange(3ossl), d2i_AUTHORITY_INFO_ACCESS(3ossl), d2i_AUTHORITY_KEYID(3ossl), d2i_BASIC_CONSTRAINTS(3ossl), d2i_CERTIFICATEPOLICIES(3ossl), d2i_CMS_ContentInfo(3ossl), d2i_CMS_ReceiptRequest(3ossl), d2i_CMS_bio(3ossl), d2i_CRL_DIST_POINTS(3ossl), d2i_DHxparams(3ossl), d2i_DIRECTORYSTRING(3ossl), d2i_DISPLAYTEXT(3ossl), d2i_DIST_POINT(3ossl), d2i_DIST_POINT_NAME(3ossl), d2i_DSA_SIG(3ossl), d2i_ECDSA_SIG(3ossl), d2i_EDIPARTYNAME(3ossl), d2i_ESS_CERT_ID(3ossl), d2i_ESS_CERT_ID_V2(3ossl), d2i_ESS_ISSUER_SERIAL(3ossl), d2i_ESS_SIGNING_CERT(3ossl), d2i_ESS_SIGNING_CERT_V2(3ossl), d2i_EXTENDED_KEY_USAGE(3ossl), d2i_GENERAL_NAME(3ossl), d2i_GENERAL_NAMES(3ossl), d2i_IPAddressChoice(3ossl), d2i_IPAddressFamily(3ossl), d2i_IPAddressOrRange(3ossl), d2i_IPAddressRange(3ossl), d2i_ISSUER_SIGN_TOOL(3ossl), d2i_ISSUING_DIST_POINT(3ossl), d2i_NAMING_AUTHORITY(3ossl), d2i_NETSCAPE_CERT_SEQUENCE(3ossl), d2i_NETSCAPE_SPKAC(3ossl), d2i_NETSCAPE_SPKI(3ossl), d2i_NOTICEREF(3ossl), d2i_OCSP_BASICRESP(3ossl), d2i_OCSP_CERTID(3ossl), d2i_OCSP_CERTSTATUS(3ossl), d2i_OCSP_CRLID(3ossl), d2i_OCSP_ONEREQ(3ossl), d2i_OCSP_REQINFO(3ossl), d2i_OCSP_REQUEST(3ossl), d2i_OCSP_RESPBYTES(3ossl), d2i_OCSP_RESPDATA(3ossl), d2i_OCSP_RESPID(3ossl), d2i_OCSP_RESPONSE(3ossl), d2i_OCSP_REVOKEDINFO(3ossl), d2i_OCSP_SERVICELOC(3ossl), d2i_OCSP_SIGNATURE(3ossl), d2i_OCSP_SINGLERESP(3ossl), d2i_OSSL_CMP_MSG(3ossl), d2i_OSSL_CMP_PKIHEADER(3ossl), d2i_OSSL_CMP_PKISI(3ossl), d2i_OSSL_CRMF_CERTID(3ossl), d2i_OSSL_CRMF_CERTTEMPLATE(3ossl), d2i_OSSL_CRMF_ENCRYPTEDVALUE(3ossl), d2i_OSSL_CRMF_MSG(3ossl), d2i_OSSL_CRMF_MSGS(3ossl), d2i_OSSL_CRMF_PBMPARAMETER(3ossl), d2i_OSSL_CRMF_PKIPUBLICATIONINFO(3ossl), d2i_OSSL_CRMF_SINGLEPUBINFO(3ossl), d2i_OTHERNAME(3ossl), d2i_PBE2PARAM(3ossl), d2i_PBEPARAM(3ossl), d2i_PBKDF2PARAM(3ossl), d2i_PKCS12(3ossl), d2i_PKCS12_BAGS(3ossl), d2i_PKCS12_MAC_DATA(3ossl), d2i_PKCS12_SAFEBAG(3ossl), d2i_PKCS12_bio(3ossl), d2i_PKCS12_fp(3ossl), d2i_PKCS7(3ossl), d2i_PKCS7_DIGEST(3ossl), d2i_PKCS7_ENCRYPT(3ossl), d2i_PKCS7_ENC_CONTENT(3ossl), d2i_PKCS7_ENVELOPE(3ossl), d2i_PKCS7_ISSUER_AND_SERIAL(3ossl), d2i_PKCS7_RECIP_INFO(3ossl), d2i_PKCS7_SIGNED(3ossl), d2i_PKCS7_SIGNER_INFO(3ossl), d2i_PKCS7_SIGN_ENVELOPE(3ossl), d2i_PKCS7_bio(3ossl), d2i_PKCS7_fp(3ossl), d2i_PKCS8_PRIV_KEY_INFO(3ossl), d2i_PKCS8_PRIV_KEY_INFO_bio(3ossl), d2i_PKCS8_PRIV_KEY_INFO_fp(3ossl), d2i_PKCS8_bio(3ossl), d2i_PKCS8_fp(3ossl), d2i_PKEY_USAGE_PERIOD(3ossl), d2i_POLICYINFO(3ossl), d2i_POLICYQUALINFO(3ossl), d2i_PROFESSION_INFO(3ossl), d2i_PROXY_CERT_INFO_EXTENSION(3ossl), d2i_PROXY_POLICY(3ossl), d2i_RSA_OAEP_PARAMS(3ossl), d2i_RSA_PSS_PARAMS(3ossl), d2i_SCRYPT_PARAMS(3ossl), d2i_SCT_LIST(3ossl), d2i_SXNET(3ossl), d2i_SXNETID(3ossl), d2i_TS_ACCURACY(3ossl), d2i_TS_MSG_IMPRINT(3ossl), d2i_TS_MSG_IMPRINT_bio(3ossl), d2i_TS_MSG_IMPRINT_fp(3ossl), d2i_TS_REQ(3ossl), d2i_TS_REQ_bio(3ossl), d2i_TS_REQ_fp(3ossl), d2i_TS_RESP(3ossl), d2i_TS_RESP_bio(3ossl), d2i_TS_RESP_fp(3ossl), d2i_TS_STATUS_INFO(3ossl), d2i_TS_TST_INFO(3ossl), d2i_TS_TST_INFO_bio(3ossl), d2i_TS_TST_INFO_fp(3ossl), d2i_USERNOTICE(3ossl), d2i_X509(3ossl), d2i_X509_bio(3ossl), d2i_X509_fp(3ossl), d2i_X509_ALGOR(3ossl), d2i_X509_ALGORS(3ossl), d2i_X509_ATTRIBUTE(3ossl), d2i_X509_CERT_AUX(3ossl), d2i_X509_CINF(3ossl), d2i_X509_CRL(3ossl), d2i_X509_CRL_INFO(3ossl), d2i_X509_CRL_bio(3ossl), d2i_X509_CRL_fp(3ossl), d2i_X509_EXTENSION(3ossl), d2i_X509_EXTENSIONS(3ossl), d2i_X509_NAME(3ossl), d2i_X509_NAME_ENTRY(3ossl), d2i_X509_PUBKEY(3ossl), d2i_X509_PUBKEY_bio(3ossl), d2i_X509_PUBKEY_fp(3ossl), d2i_X509_REQ(3ossl), d2i_X509_REQ_INFO(3ossl), d2i_X509_REQ_bio(3ossl), d2i_X509_REQ_fp(3ossl), d2i_X509_REVOKED(3ossl), d2i_X509_SIG(3ossl), d2i_X509_VAL(3ossl), i2d_ACCESS_DESCRIPTION(3ossl), i2d_ADMISSIONS(3ossl), i2d_ADMISSION_SYNTAX(3ossl), i2d_ASIdOrRange(3ossl), i2d_ASIdentifierChoice(3ossl), i2d_ASIdentifiers(3ossl), i2d_ASN1_BIT_STRING(3ossl), i2d_ASN1_BMPSTRING(3ossl), i2d_ASN1_ENUMERATED(3ossl), i2d_ASN1_GENERALIZEDTIME(3ossl), i2d_ASN1_GENERALSTRING(3ossl), i2d_ASN1_IA5STRING(3ossl), i2d_ASN1_INTEGER(3ossl), i2d_ASN1_NULL(3ossl), i2d_ASN1_OBJECT(3ossl), i2d_ASN1_OCTET_STRING(3ossl), i2d_ASN1_PRINTABLE(3ossl), i2d_ASN1_PRINTABLESTRING(3ossl), i2d_ASN1_SEQUENCE_ANY(3ossl), i2d_ASN1_SET_ANY(3ossl), i2d_ASN1_T61STRING(3ossl), i2d_ASN1_TIME(3ossl), i2d_ASN1_TYPE(3ossl), i2d_ASN1_UNIVERSALSTRING(3ossl), i2d_ASN1_UTCTIME(3ossl), i2d_ASN1_UTF8STRING(3ossl), i2d_ASN1_VISIBLESTRING(3ossl), i2d_ASN1_bio_stream(3ossl), i2d_ASRange(3ossl), i2d_AUTHORITY_INFO_ACCESS(3ossl), i2d_AUTHORITY_KEYID(3ossl), i2d_BASIC_CONSTRAINTS(3ossl), i2d_CERTIFICATEPOLICIES(3ossl), i2d_CMS_ContentInfo(3ossl), i2d_CMS_ReceiptRequest(3ossl), i2d_CMS_bio(3ossl), i2d_CRL_DIST_POINTS(3ossl), i2d_DHxparams(3ossl), i2d_DIRECTORYSTRING(3ossl), i2d_DISPLAYTEXT(3ossl), i2d_DIST_POINT(3ossl), i2d_DIST_POINT_NAME(3ossl), i2d_DSA_SIG(3ossl), i2d_ECDSA_SIG(3ossl), i2d_EDIPARTYNAME(3ossl), i2d_ESS_CERT_ID(3ossl), i2d_ESS_CERT_ID_V2(3ossl), i2d_ESS_ISSUER_SERIAL(3ossl), i2d_ESS_SIGNING_CERT(3ossl), i2d_ESS_SIGNING_CERT_V2(3ossl), i2d_EXTENDED_KEY_USAGE(3ossl), i2d_GENERAL_NAME(3ossl), i2d_GENERAL_NAMES(3ossl), i2d_IPAddressChoice(3ossl), i2d_IPAddressFamily(3ossl), i2d_IPAddressOrRange(3ossl), i2d_IPAddressRange(3ossl), i2d_ISSUER_SIGN_TOOL(3ossl), i2d_ISSUING_DIST_POINT(3ossl), i2d_NAMING_AUTHORITY(3ossl), i2d_NETSCAPE_CERT_SEQUENCE(3ossl), i2d_NETSCAPE_SPKAC(3ossl), i2d_NETSCAPE_SPKI(3ossl), i2d_NOTICEREF(3ossl), i2d_OCSP_BASICRESP(3ossl), i2d_OCSP_CERTID(3ossl), i2d_OCSP_CERTSTATUS(3ossl), i2d_OCSP_CRLID(3ossl), i2d_OCSP_ONEREQ(3ossl), i2d_OCSP_REQINFO(3ossl), i2d_OCSP_REQUEST(3ossl), i2d_OCSP_RESPBYTES(3ossl), i2d_OCSP_RESPDATA(3ossl), i2d_OCSP_RESPID(3ossl), i2d_OCSP_RESPONSE(3ossl), i2d_OCSP_REVOKEDINFO(3ossl), i2d_OCSP_SERVICELOC(3ossl), i2d_OCSP_SIGNATURE(3ossl), i2d_OCSP_SINGLERESP(3ossl), i2d_OSSL_CMP_MSG(3ossl), i2d_OSSL_CMP_PKIHEADER(3ossl), i2d_OSSL_CMP_PKISI(3ossl), i2d_OSSL_CRMF_CERTID(3ossl), i2d_OSSL_CRMF_CERTTEMPLATE(3ossl), i2d_OSSL_CRMF_ENCRYPTEDVALUE(3ossl), i2d_OSSL_CRMF_MSG(3ossl), i2d_OSSL_CRMF_MSGS(3ossl), i2d_OSSL_CRMF_PBMPARAMETER(3ossl), i2d_OSSL_CRMF_PKIPUBLICATIONINFO(3ossl), i2d_OSSL_CRMF_SINGLEPUBINFO(3ossl), i2d_OTHERNAME(3ossl), i2d_PBE2PARAM(3ossl), i2d_PBEPARAM(3ossl), i2d_PBKDF2PARAM(3ossl), i2d_PKCS12(3ossl), i2d_PKCS12_BAGS(3ossl), i2d_PKCS12_MAC_DATA(3ossl), i2d_PKCS12_SAFEBAG(3ossl), i2d_PKCS12_bio(3ossl), i2d_PKCS12_fp(3ossl), i2d_PKCS7(3ossl), i2d_PKCS7_DIGEST(3ossl), i2d_PKCS7_ENCRYPT(3ossl), i2d_PKCS7_ENC_CONTENT(3ossl), i2d_PKCS7_ENVELOPE(3ossl), i2d_PKCS7_ISSUER_AND_SERIAL(3ossl), i2d_PKCS7_NDEF(3ossl), i2d_PKCS7_RECIP_INFO(3ossl), i2d_PKCS7_SIGNED(3ossl), i2d_PKCS7_SIGNER_INFO(3ossl), i2d_PKCS7_SIGN_ENVELOPE(3ossl), i2d_PKCS7_bio(3ossl), i2d_PKCS7_fp(3ossl), i2d_PKCS8PrivateKeyInfo_bio(3ossl), i2d_PKCS8PrivateKeyInfo_fp(3ossl), i2d_PKCS8_PRIV_KEY_INFO(3ossl), i2d_PKCS8_PRIV_KEY_INFO_bio(3ossl), i2d_PKCS8_PRIV_KEY_INFO_fp(3ossl), i2d_PKCS8_bio(3ossl), i2d_PKCS8_fp(3ossl), i2d_PKEY_USAGE_PERIOD(3ossl), i2d_POLICYINFO(3ossl), i2d_POLICYQUALINFO(3ossl), i2d_PROFESSION_INFO(3ossl), i2d_PROXY_CERT_INFO_EXTENSION(3ossl), i2d_PROXY_POLICY(3ossl), i2d_RSA_OAEP_PARAMS(3ossl), i2d_RSA_PSS_PARAMS(3ossl), i2d_SCRYPT_PARAMS(3ossl), i2d_SCT_LIST(3ossl), i2d_SXNET(3ossl), i2d_SXNETID(3ossl), i2d_TS_ACCURACY(3ossl), i2d_TS_MSG_IMPRINT(3ossl), i2d_TS_MSG_IMPRINT_bio(3ossl), i2d_TS_MSG_IMPRINT_fp(3ossl), i2d_TS_REQ(3ossl), i2d_TS_REQ_bio(3ossl), i2d_TS_REQ_fp(3ossl), i2d_TS_RESP(3ossl), i2d_TS_RESP_bio(3ossl), i2d_TS_RESP_fp(3ossl), i2d_TS_STATUS_INFO(3ossl), i2d_TS_TST_INFO(3ossl), i2d_TS_TST_INFO_bio(3ossl), i2d_TS_TST_INFO_fp(3ossl), i2d_USERNOTICE(3ossl), i2d_X509(3ossl), i2d_X509_bio(3ossl), i2d_X509_fp(3ossl), i2d_X509_ALGOR(3ossl), i2d_X509_ALGORS(3ossl), i2d_X509_ATTRIBUTE(3ossl), i2d_X509_CERT_AUX(3ossl), i2d_X509_CINF(3ossl), i2d_X509_CRL(3ossl), i2d_X509_CRL_INFO(3ossl), i2d_X509_CRL_bio(3ossl), i2d_X509_CRL_fp(3ossl), i2d_X509_EXTENSION(3ossl), i2d_X509_EXTENSIONS(3ossl), i2d_X509_NAME(3ossl), i2d_X509_NAME_ENTRY(3ossl), i2d_X509_PUBKEY(3ossl), i2d_X509_PUBKEY_bio(3ossl), i2d_X509_PUBKEY_fp(3ossl), i2d_X509_REQ(3ossl), i2d_X509_REQ_INFO(3ossl), i2d_X509_REQ_bio(3ossl), i2d_X509_REQ_fp(3ossl), i2d_X509_REVOKED(3ossl), i2d_X509_SIG(3ossl), i2d_X509_VAL(3ossl)
convert objects from/to ASN.1/DER representation
d2i_DSAPrivateKey(3ossl), d2i_DSAPrivateKey_bio(3ossl), d2i_DSAPrivateKey_fp(3ossl), d2i_DSAPublicKey(3ossl), d2i_DSA_PUBKEY(3ossl), d2i_DSA_PUBKEY_bio(3ossl), d2i_DSA_PUBKEY_fp(3ossl), d2i_DSAparams(3ossl), d2i_RSAPrivateKey(3ossl), d2i_RSAPrivateKey_bio(3ossl), d2i_RSAPrivateKey_fp(3ossl), d2i_RSAPublicKey(3ossl), d2i_RSAPublicKey_bio(3ossl), d2i_RSAPublicKey_fp(3ossl), d2i_RSA_PUBKEY(3ossl), d2i_RSA_PUBKEY_bio(3ossl), d2i_RSA_PUBKEY_fp(3ossl), d2i_DHparams(3ossl), d2i_DHparams_bio(3ossl), d2i_DHparams_fp(3ossl), d2i_ECPKParameters(3ossl), d2i_ECParameters(3ossl), d2i_ECPrivateKey(3ossl), d2i_ECPrivateKey_bio(3ossl), d2i_ECPrivateKey_fp(3ossl), d2i_EC_PUBKEY(3ossl), d2i_EC_PUBKEY_bio(3ossl), d2i_EC_PUBKEY_fp(3ossl), i2d_RSAPrivateKey(3ossl), i2d_RSAPrivateKey_bio(3ossl), i2d_RSAPrivateKey_fp(3ossl), i2d_RSAPublicKey(3ossl), i2d_RSAPublicKey_bio(3ossl), i2d_RSAPublicKey_fp(3ossl), i2d_RSA_PUBKEY(3ossl), i2d_RSA_PUBKEY_bio(3ossl), i2d_RSA_PUBKEY_fp(3ossl), i2d_DHparams(3ossl), i2d_DHparams_bio(3ossl), i2d_DHparams_fp(3ossl), i2d_DSAPrivateKey(3ossl), i2d_DSAPrivateKey_bio(3ossl), i2d_DSAPrivateKey_fp(3ossl), i2d_DSAPublicKey(3ossl), i2d_DSA_PUBKEY(3ossl), i2d_DSA_PUBKEY_bio(3ossl), i2d_DSA_PUBKEY_fp(3ossl), i2d_DSAparams(3ossl), i2d_ECPKParameters(3ossl), i2d_ECParameters(3ossl), i2d_ECPrivateKey(3ossl), i2d_ECPrivateKey_bio(3ossl), i2d_ECPrivateKey_fp(3ossl), i2d_EC_PUBKEY(3ossl), i2d_EC_PUBKEY_bio(3ossl), i2d_EC_PUBKEY_fp(3ossl)
DEPRECATED
d2i_PKCS8PrivateKey_bio(3), d2i_PKCS8PrivateKey_fp(3), i2d_PKCS8PrivateKey_bio(3), i2d_PKCS8PrivateKey_fp(3), i2d_PKCS8PrivateKey_nid_bio(3), i2d_PKCS8PrivateKey_nid_fp(3)
PKCS#8 format private key functions
d2i_PKCS8PrivateKey_bio(3ossl), d2i_PKCS8PrivateKey_fp(3ossl), i2d_PKCS8PrivateKey_bio(3ossl), i2d_PKCS8PrivateKey_fp(3ossl), i2d_PKCS8PrivateKey_nid_bio(3ossl), i2d_PKCS8PrivateKey_nid_fp(3ossl)
PKCS#8 format private key functions
d2i_PrivateKey(3), d2i_PublicKey(3), d2i_AutoPrivateKey(3), i2d_PrivateKey(3), i2d_PublicKey(3), d2i_PrivateKey_bio(3), d2i_PrivateKey_fp(3)
decode and encode functions for reading and saving EVP_PKEY structures
d2i_PrivateKey_ex(3ossl), d2i_PrivateKey(3ossl), d2i_PublicKey(3ossl), d2i_KeyParams(3ossl), d2i_AutoPrivateKey_ex(3ossl), d2i_AutoPrivateKey(3ossl), i2d_PrivateKey(3ossl), i2d_PublicKey(3ossl), i2d_KeyParams(3ossl), i2d_KeyParams_bio(3ossl), d2i_PrivateKey_ex_bio(3ossl), d2i_PrivateKey_bio(3ossl), d2i_PrivateKey_ex_fp(3ossl), d2i_PrivateKey_fp(3ossl), d2i_KeyParams_bio(3ossl), i2d_PrivateKey_bio(3ossl), i2d_PrivateKey_fp(3ossl)
decode and encode functions for reading and saving EVP_PKEY structures
d2i_of_void(3), PEM_ASN1_read(3), PEM_ASN1_read_bio(3)
PEM and DER decode an arbitrary ASN.1 value
default_palette(3)
The default IBM BIOS palette. Allegro game programming library
fido_bio_dev_get_info(3), fido_bio_dev_enroll_begin(3), fido_bio_dev_enroll_continue(3), fido_bio_dev_enroll_cancel(3), fido_bio_dev_enroll_remove(3), fido_bio_dev_get_template_array(3), fido_bio_dev_set_template_name(3)
FIDO2 biometric authenticator API
fido_bio_enroll_new(3), fido_bio_enroll_free(3), fido_bio_enroll_last_status(3), fido_bio_enroll_remaining_samples(3)
FIDO2 biometric enrollment API
fido_bio_info_new(3), fido_bio_info_free(3), fido_bio_info_type(3), fido_bio_info_max_samples(3)
FIDO2 biometric sensor information API
fido_bio_template(3), fido_bio_template_array_count(3), fido_bio_template_array_free(3), fido_bio_template_array_new(3), fido_bio_template_free(3), fido_bio_template_id_len(3), fido_bio_template_id_ptr(3), fido_bio_template_name(3), fido_bio_template_new(3), fido_bio_template_set_id(3), fido_bio_template_set_name(3)
FIDO2 biometric template API
grub-bios-setup(8)
set up a device to boot using GRUB
hmmer(1), HMMER(1)
profile HMMs for biological sequence analysis
i2d_CMS_bio_stream(3)
output CMS_ContentInfo structure in BER format
i2d_CMS_bio_stream(3ossl)
output CMS_ContentInfo structure in BER format
i2d_PKCS7_bio_stream(3)
output PKCS7 structure in BER format
i2d_PKCS7_bio_stream(3ossl)
output PKCS7 structure in BER format
idfetch(1)
retrieve biological data from the NCBI ID1 server
lh_stats(3), lh_node_stats(3), lh_node_usage_stats(3), lh_stats_bio(3), lh_node_stats_bio(3), lh_node_usage_stats_bio(3)
LHASH statistics
lmhosts(5)
The Samba NetBIOS hosts file
load_bios_font(3)
Loads a 8x8 or 8x16 BIOS format font. Allegro game programming library
load_grx_or_bios_font(3)
Loads either a BIOS or GRX format font. Allegro game programming library
makeset(1)
build a Bioseq-set from Seq-entries
mexSLOAD(1)
a mex-functions for loading biomedical signal data into Octave or Matlab
nbtscan(1)
scan networks for NetBIOS name information
nmbd(8)
NetBIOS name server to provide NetBIOS over IP naming services to clients
nmblookup(1)
NetBIOS over TCP/IP client used to lookup NetBIOS names
pem_password_cb(3), PEM_read_bio_PrivateKey(3), PEM_read_PrivateKey(3), PEM_write_bio_PrivateKey(3), PEM_write_bio_PrivateKey_traditional(3), PEM_write_PrivateKey(3), PEM_write_bio_PKCS8PrivateKey(3), PEM_write_PKCS8PrivateKey(3), PEM_write_bio_PKCS8PrivateKey_nid(3), PEM_write_PKCS8PrivateKey_nid(3), PEM_read_bio_PUBKEY(3), PEM_read_PUBKEY(3), PEM_write_bio_PUBKEY(3), PEM_write_PUBKEY(3), PEM_read_bio_RSAPrivateKey(3), PEM_read_RSAPrivateKey(3), PEM_write_bio_RSAPrivateKey(3), PEM_write_RSAPrivateKey(3), PEM_read_bio_RSAPublicKey(3), PEM_read_RSAPublicKey(3), PEM_write_bio_RSAPublicKey(3), PEM_write_RSAPublicKey(3), PEM_read_bio_RSA_PUBKEY(3), PEM_read_RSA_PUBKEY(3), PEM_write_bio_RSA_PUBKEY(3), PEM_write_RSA_PUBKEY(3), PEM_read_bio_DSAPrivateKey(3), PEM_read_DSAPrivateKey(3), PEM_write_bio_DSAPrivateKey(3), PEM_write_DSAPrivateKey(3), PEM_read_bio_DSA_PUBKEY(3), PEM_read_DSA_PUBKEY(3), PEM_write_bio_DSA_PUBKEY(3), PEM_write_DSA_PUBKEY(3), PEM_read_bio_Parameters(3), PEM_write_bio_Parameters(3), PEM_read_bio_DSAparams(3), PEM_read_DSAparams(3), PEM_write_bio_DSAparams(3), PEM_write_DSAparams(3), PEM_read_bio_DHparams(3), PEM_read_DHparams(3), PEM_write_bio_DHparams(3), PEM_write_DHparams(3), PEM_read_bio_X509(3), PEM_read_X509(3), PEM_write_bio_X509(3), PEM_write_X509(3), PEM_read_bio_X509_AUX(3), PEM_read_X509_AUX(3), PEM_write_bio_X509_AUX(3), PEM_write_X509_AUX(3), PEM_read_bio_X509_REQ(3), PEM_read_X509_REQ(3), PEM_write_bio_X509_REQ(3), PEM_write_X509_REQ(3), PEM_write_bio_X509_REQ_NEW(3), PEM_write_X509_REQ_NEW(3), PEM_read_bio_X509_CRL(3), PEM_read_X509_CRL(3), PEM_write_bio_X509_CRL(3), PEM_write_X509_CRL(3), PEM_read_bio_PKCS7(3), PEM_read_PKCS7(3), PEM_write_bio_PKCS7(3), PEM_write_PKCS7(3)
PEM routines
pem_password_cb(3ossl), PEM_read_bio_PrivateKey_ex(3ossl), PEM_read_bio_PrivateKey(3ossl), PEM_read_PrivateKey_ex(3ossl), PEM_read_PrivateKey(3ossl), PEM_write_bio_PrivateKey_ex(3ossl), PEM_write_bio_PrivateKey(3ossl), PEM_write_bio_PrivateKey_traditional(3ossl), PEM_write_PrivateKey_ex(3ossl), PEM_write_PrivateKey(3ossl), PEM_write_bio_PKCS8PrivateKey(3ossl), PEM_write_PKCS8PrivateKey(3ossl), PEM_write_bio_PKCS8PrivateKey_nid(3ossl), PEM_write_PKCS8PrivateKey_nid(3ossl), PEM_read_bio_PUBKEY_ex(3ossl), PEM_read_bio_PUBKEY(3ossl), PEM_read_PUBKEY_ex(3ossl), PEM_read_PUBKEY(3ossl), PEM_write_bio_PUBKEY_ex(3ossl), PEM_write_bio_PUBKEY(3ossl), PEM_write_PUBKEY_ex(3ossl), PEM_write_PUBKEY(3ossl), PEM_read_bio_RSAPrivateKey(3ossl), PEM_read_RSAPrivateKey(3ossl), PEM_write_bio_RSAPrivateKey(3ossl), PEM_write_RSAPrivateKey(3ossl), PEM_read_bio_RSAPublicKey(3ossl), PEM_read_RSAPublicKey(3ossl), PEM_write_bio_RSAPublicKey(3ossl), PEM_write_RSAPublicKey(3ossl), PEM_read_bio_RSA_PUBKEY(3ossl), PEM_read_RSA_PUBKEY(3ossl), PEM_write_bio_RSA_PUBKEY(3ossl), PEM_write_RSA_PUBKEY(3ossl), PEM_read_bio_DSAPrivateKey(3ossl), PEM_read_DSAPrivateKey(3ossl), PEM_write_bio_DSAPrivateKey(3ossl), PEM_write_DSAPrivateKey(3ossl), PEM_read_bio_DSA_PUBKEY(3ossl), PEM_read_DSA_PUBKEY(3ossl), PEM_write_bio_DSA_PUBKEY(3ossl), PEM_write_DSA_PUBKEY(3ossl), PEM_read_bio_Parameters_ex(3ossl), PEM_read_bio_Parameters(3ossl), PEM_write_bio_Parameters(3ossl), PEM_read_bio_DSAparams(3ossl), PEM_read_DSAparams(3ossl), PEM_write_bio_DSAparams(3ossl), PEM_write_DSAparams(3ossl), PEM_read_bio_DHparams(3ossl), PEM_read_DHparams(3ossl), PEM_write_bio_DHparams(3ossl), PEM_write_DHparams(3ossl), PEM_read_bio_X509(3ossl), PEM_read_X509(3ossl), PEM_write_bio_X509(3ossl), PEM_write_X509(3ossl), PEM_read_bio_X509_AUX(3ossl), PEM_read_X509_AUX(3ossl), PEM_write_bio_X509_AUX(3ossl), PEM_write_X509_AUX(3ossl), PEM_read_bio_X509_REQ(3ossl), PEM_read_X509_REQ(3ossl), PEM_write_bio_X509_REQ(3ossl), PEM_write_X509_REQ(3ossl), PEM_write_bio_X509_REQ_NEW(3ossl), PEM_write_X509_REQ_NEW(3ossl), PEM_read_bio_X509_CRL(3ossl), PEM_read_X509_CRL(3ossl), PEM_write_bio_X509_CRL(3ossl), PEM_write_X509_CRL(3ossl), PEM_read_bio_PKCS7(3ossl), PEM_read_PKCS7(3ossl), PEM_write_bio_PKCS7(3ossl), PEM_write_PKCS7(3ossl)
PEM routines
rec2bin(1)
converts biosignal data into a header file in ASCII format, and a binary file for every channel
save2gdf(1)
converts different biomedical signal file formats
sigviewer(1), SigViewer(1)
a viewing and scoring tools for biomedical signals
udv(1)
OneD-Viewer for biological sequences
ugene(1), UGENE(1)
integrated bioinformatics suite
vbetool(1)
run real-mode video BIOS code to alter hardware state
vsearch(1)
a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pairwise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics
App::Netdisco::AnyEvent::Nbtstat(3)
Request NetBIOS node status with AnyEvent
Bio::ASN1::EntrezGene(3)
Regular expression-based Perl Parser for NCBI Entrez Gene
Bio::ASN1::EntrezGene::Indexer(3)
Indexes NCBI Sequence files
Bio::ASN1::Sequence(3)
Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences
Bio::ASN1::Sequence::Indexer(3)
Indexes NCBI Sequence files
Bio::Align::AlignI(3)
An interface for describing sequence alignments
Bio::Align::DNAStatistics(3)
Calculate some statistics for a DNA alignment
Bio::Align::PairwiseStatistics(3)
Base statistic object for Pairwise Alignments
Bio::Align::ProteinStatistics(3)
Calculate Protein Alignment statistics (mostly distances)
Bio::Align::StatisticsI(3)
Calculate some statistics for an alignment
Bio::Align::Utilities(3)
A collection of utilities regarding converting and manipulating alignment objects
Bio::AlignIO(3)
Handler for AlignIO Formats
Bio::AlignIO::Handler::GenericAlignHandler(3)
Bio::HandlerI-based generic data handler class for alignment-based data
Bio::AlignIO::arp(3)
ARP MSA Sequence input/output stream
Bio::AlignIO::bl2seq(3)
bl2seq sequence input/output stream
Bio::AlignIO::clustalw(3)
clustalw sequence input/output stream
Bio::AlignIO::emboss(3)
Parse EMBOSS alignment output (from applications water and needle)
Bio::AlignIO::fasta(3)
fasta MSA Sequence input/output stream
Bio::AlignIO::largemultifasta(3)
Largemultifasta MSA Sequence input/output stream
Bio::AlignIO::maf(3)
Multiple Alignment Format sequence input stream
Bio::AlignIO::mase(3)
mase sequence input/output stream
Bio::AlignIO::mega(3)
Parse and Create MEGA format data files
Bio::AlignIO::meme(3)
meme sequence input/output stream
Bio::AlignIO::metafasta(3)
Metafasta MSA Sequence input/output stream
Bio::AlignIO::msf(3)
msf sequence input/output stream
Bio::AlignIO::nexus(3)
NEXUS format sequence input/output stream
Bio::AlignIO::pfam(3)
pfam sequence input/output stream
Bio::AlignIO::phylip(3)
PHYLIP format sequence input/output stream
Bio::AlignIO::po(3)
po MSA Sequence input/output stream
Bio::AlignIO::proda(3)
proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu)
Bio::AlignIO::prodom(3)
prodom sequence input/output stream
Bio::AlignIO::psi(3)
Read/Write PSI-BLAST profile alignment files
Bio::AlignIO::selex(3)
selex sequence input/output stream
Bio::AlignIO::xmfa(3)
XMFA MSA Sequence input/output stream
Bio::AnalysisI(3)
An interface to any (local or remote) analysis tool
Bio::AnalysisParserI(3)
Generic analysis output parser interface
Bio::AnalysisResultI(3)
Interface for analysis result objects
Bio::AnnotatableI(3)
the base interface an annotatable object must implement
Bio::Annotation::AnnotationFactory(3)
Instantiates a new Bio::AnnotationI (or derived class) through a factory
Bio::Annotation::Collection(3)
Default Perl implementation of AnnotationCollectionI
Bio::Annotation::Comment(3)
A comment object, holding text
Bio::Annotation::DBLink(3)
untyped links between databases
Bio::Annotation::OntologyTerm(3)
An ontology term adapted to AnnotationI
Bio::Annotation::Reference(3)
Specialised DBLink object for Literature References
Bio::Annotation::Relation(3)
Relationship (pairwise) with other objects SeqI and NodeI;
Bio::Annotation::SimpleValue(3)
A simple scalar
Bio::Annotation::StructuredValue(3)
A scalar with embedded structured information
Bio::Annotation::TagTree(3)
AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text
Bio::Annotation::Target(3)
Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Bio::Annotation::Tree(3)
Provide a tree as an annotation to a Bio::AnnotatableI object
Bio::Annotation::TypeManager(3)
Manages types for annotation collections
Bio::AnnotationCollectionI(3)
Interface for annotation collections
Bio::AnnotationI(3)
Annotation interface
Bio::Cluster(3)
BioPerl cluster modules
Bio::Cluster::ClusterFactory(3)
Instantiates a new Bio::ClusterI (or derived class) through a factory
Bio::Cluster::FamilyI(3)
Family Interface
Bio::Cluster::SequenceFamily(3)
Sequence Family object
Bio::Cluster::UniGene(3)
UniGene object
Bio::Cluster::UniGeneI(3)
abstract interface of UniGene object
Bio::ClusterI(3)
Cluster Interface
Bio::ClusterIO(3)
Handler for Cluster Formats
Bio::ClusterIO::dbsnp(3)
dbSNP input stream
Bio::ClusterIO::unigene(3)
UniGene input stream
Bio::CodonUsage::IO(3)
for reading and writing codon usage tables to file
Bio::CodonUsage::Table(3)
for access to the Codon usage Database at http://www.kazusa.or.jp/codon
Bio::Coordinate(3)
Modules for working with biological coordinates
Bio::Coordinate::Chain(3)
Mapping locations through a chain of coordinate mappers
Bio::Coordinate::Collection(3)
Noncontinuous match between two coordinate sets
Bio::Coordinate::ExtrapolatingPair(3)
Continuous match between two coordinate sets
Bio::Coordinate::GeneMapper(3)
Transformations between gene related coordinate systems
Bio::Coordinate::Graph(3)
Finds shortest path between nodes in a graph
Bio::Coordinate::MapperI(3)
Interface describing coordinate mappers
Bio::Coordinate::Pair(3)
Continuous match between two coordinate sets
Bio::Coordinate::Result(3)
Results from coordinate transformation
Bio::Coordinate::Result::Gap(3)
Another name for Bio::Location::Simple
Bio::Coordinate::Result::Match(3)
Another name for Bio::Location::Simple
Bio::Coordinate::ResultI(3)
Interface to identify coordinate mapper results
Bio::Coordinate::Utils(3)
Additional methods to create Bio::Coordinate objects
Bio::DB::DBFetch(3)
Database object for retrieving using the dbfetch script
Bio::DB::EMBL(3)
Database object interface for EMBL entry retrieval
Bio::DB::ESoap(3)
Client for the NCBI Entrez EUtilities SOAP server
Bio::DB::ESoap::WSDL(3)
WSDL parsing for Entrez SOAP EUtilities
Bio::DB::EntrezGene(3)
Database object interface to Entrez Gene
Bio::DB::Failover(3)
A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
Bio::DB::Fasta(3)
Fast indexed access to fasta files
Bio::DB::FileCache(3)
In file cache for BioSeq objects
Bio::DB::Flat(3)
Interface for indexed flat files
Bio::DB::Flat::BDB(3)
Interface for BioHackathon standard BDB-indexed flat file
Bio::DB::Flat::BDB::embl(3)
embl adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::fasta(3)
fasta adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::genbank(3)
genbank adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::swiss(3)
swissprot adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BinarySearch(3)
BinarySearch search indexing system for sequence files
Bio::DB::GFF::Util::Binning(3)
binning utility for Bio::DB::GFF index
Bio::DB::GFF::Util::Rearrange(3)
rearrange utility
Bio::DB::GenBank(3)
Database object interface to GenBank
Bio::DB::GenPept(3)
Database object interface to GenPept
Bio::DB::GenericWebAgent(3)
helper base class for parameter-based remote server access and response retrieval
Bio::DB::InMemoryCache(3)
Abstract interface for a sequence database
Bio::DB::IndexedBase(3)
Base class for modules using indexed sequence files
Bio::DB::LocationI(3)
A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
Bio::DB::NCBIHelper(3)
A collection of routines useful for queries to NCBI databases
Bio::DB::Qual(3)
Fast indexed access to quality files
Bio::DB::Query::GenBank(3)
Build a GenBank Entrez Query
Bio::DB::Query::WebQuery(3)
Helper class for web-based sequence queryies
Bio::DB::QueryI(3)
Object Interface to queryable sequence databases
Bio::DB::RandomAccessI(3)
Abstract interface for a sequence database
Bio::DB::ReferenceI(3)
A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
Bio::DB::Registry(3)
Access to the Open Bio Database Access registry scheme
Bio::DB::SeqI(3)
Abstract Interface for Sequence databases
Bio::DB::SoapEUtilities(3)
Interface to the NCBI Entrez web service *BETA*
Bio::DB::SoapEUtilities::DocSumAdaptor(3)
Handle for Entrez SOAP DocSums
Bio::DB::SoapEUtilities::FetchAdaptor(3)
Conversion of Entrez SOAP messages to BioPerl objects
Bio::DB::SoapEUtilities::FetchAdaptor::seq(3)
Fetch adaptor for 'seq' efetch SOAP messages
Bio::DB::SoapEUtilities::FetchAdaptor::species(3)
Fetch adaptor for 'taxonomy' efetch SOAP messages
Bio::DB::SoapEUtilities::GQueryAdaptor(3)
Handle for Entrez SOAP GlobalQuery items
Bio::DB::SoapEUtilities::LinkAdaptor(3)
Handle for Entrez SOAP LinkSets
Bio::DB::SoapEUtilities::Result(3)
Accessor object for SoapEUtilities results
Bio::DB::Taxonomy(3)
Access to a taxonomy database
Bio::DB::Taxonomy::entrez(3)
Taxonomy Entrez driver
Bio::DB::Taxonomy::flatfile(3)
Use the NCBI taxonomy from local indexed flat files
Bio::DB::Taxonomy::greengenes(3)
Use the Greengenes taxonomy
Bio::DB::Taxonomy::list(3)
An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
Bio::DB::Taxonomy::silva(3)
Use the Silva taxonomy
Bio::DB::UpdateableSeqI(3)
An interface for writing to a database of sequences
Bio::DB::WebDBSeqI(3)
Object Interface to generalize Web Databases for retrieving sequences
Bio::DBLinkContainerI(3)
Abstract interface for any object wanting to use database cross references
Bio::Das(3)
Interface to Distributed Annotation System
Bio::Das::DSN(3)
Object encapsulation of a DAS data source
Bio::Das::Feature(3), Bio::Das::Segment::Feature(3)
A genomic annotation
Bio::Das::FeatureIterator(3)
Iterate over a set of Bio::Das::Features
Bio::Das::FeatureTypeI(3)
Simple interface to Sequence Ontology feature types
Bio::Das::HTTP::Fetch(3)
Manage the HTTP protocol for DAS transactions
Bio::Das::Lite(3)
Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/)
Bio::Das::Map(3)
Resolve map coordinates
Bio::Das::Request(3)
Base class for a request on a DAS server
Bio::Das::Request::Dnas(3)
The DAS "dna" request
Bio::Das::Request::Dsn(3)
The DAS "dsn" request
Bio::Das::Request::Entry_points(3)
The DAS "entry_points" request
Bio::Das::Request::Feature2Segments(3)
Translate feature names into segments
Bio::Das::Request::Sequences(3)
The DAS "sequence" request
Bio::Das::Request::Stylesheet(3)
The DAS "stylesheet" request
Bio::Das::Request::Types(3)
The DAS "types" request
Bio::Das::Segment(3)
Serial access to Bio::Das sequence "segments"
Bio::Das::SegmentI(3)
DAS-style access to a feature database
Bio::Das::Stylesheet(3)
Access to DAS stylesheets
Bio::Das::Type(3)
A sequence annotation type
Bio::Das::TypeHandler(3)
-- Utilities for handling types
Bio::Das::Util(3)
Das Utilities
Bio::DasI(3)
DAS-style access to a feature database
Bio::DescribableI(3)
interface for objects with human readable names and descriptions
Bio::Event::EventGeneratorI(3)
This interface describes the basic event generator class
Bio::Event::EventHandlerI(3)
An Event Handler Interface
Bio::Factory::AnalysisI(3)
An interface to analysis tool factory
Bio::Factory::ApplicationFactoryI(3)
Interface class for Application Factories
Bio::Factory::DriverFactory(3)
Base class for factory classes loading drivers
Bio::Factory::EMBOSS(3)
EMBOSS application factory class
Bio::Factory::FTLocationFactory(3)
A FeatureTable Location Parser
Bio::Factory::LocationFactoryI(3)
A factory interface for generating locations from a string
Bio::Factory::ObjectBuilderI(3)
Interface for an object builder
Bio::Factory::ObjectFactory(3)
Instantiates a new Bio::Root::RootI (or derived class) through a factory
Bio::Factory::ObjectFactoryI(3)
A General object creator factory
Bio::Factory::SeqAnalysisParserFactory(3)
class capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SeqAnalysisParserFactoryI(3)
interface describing objects capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SequenceFactoryI(3)
This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Bio::Factory::SequenceProcessorI(3)
Interface for chained sequence processing algorithms
Bio::Factory::SequenceStreamI(3)
Interface describing the basics of a Sequence Stream
Bio::Factory::TreeFactoryI(3)
Factory Interface for getting and writing trees from/to a data stream
Bio::FeatureHolderI(3)
the base interface an object with features must implement
Bio::FeatureIO(3)
Handler for FeatureIO
Bio::FeatureIO::bed(3)
read/write features from UCSC BED format
Bio::FeatureIO::gff(3)
read/write GFF feature files
Bio::FeatureIO::gtf(3)
read write features in GTF format
Bio::FeatureIO::interpro(3)
read features from InterPro XML
Bio::FeatureIO::ptt(3)
read/write features in PTT format
Bio::FeatureIO::vecscreen_simple(3)
read/write features from NCBI vecscreen -f 3 output
Bio::GFF3::LowLevel(3)
fast, low-level functions for parsing and formatting GFF3
Bio::GFF3::LowLevel::Parser(3)
a fast, low-level gff3 parser
Bio::GFF3::LowLevel::Parser::1_0_backcompat(3)
compatibility layer to support Bio::GFF3::LowLevel::Parser 1.0 API
Bio::GFF3::Transform::FromFasta(3)
make gff3 for the sequences in a fasta file
Bio::GFF3::Transform::SyncDirectives(3)
insert sync (###) directives into an existing GFF3 file. WARNING: this module does not really work in the general case, read the DESCRIPTION section below
Bio::Glite(3)
G-language Genome Analysis Environment REST service interface module
Bio::Graphics(3)
Generate GD images of Bio::Seq objects
Bio::Graphics::ConfiguratorI(3)
A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag->value semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse)
Bio::Graphics::DrawTransmembrane(3)
draw a cartoon of an Alpha-helical transmembrane protein
Bio::Graphics::Feature(3)
A simple feature object for use with Bio::Graphics::Panel
Bio::Graphics::FeatureBase(3)
Compatibility module
Bio::Graphics::FeatureDir(3)
-- A directory of feature files and conf files
Bio::Graphics::FeatureFile(3)
-- A set of Bio::Graphics features, stored in a file
Bio::Graphics::FeatureFile::Iterator(3)
-- Iterator across a Bio::Graphics::FeatureFile
Bio::Graphics::Glyph(3)
Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::Factory(3)
Factory for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::alignment(3)
The "alignment" glyph
Bio::Graphics::Glyph::allele_tower(3)
The "allele_tower" glyph
Bio::Graphics::Glyph::anchored_arrow(3)
The "anchored_arrow" glyph
Bio::Graphics::Glyph::arrow(3)
the "arrow" glyph
Bio::Graphics::Glyph::box(3)
The "box" glyph
Bio::Graphics::Glyph::broken_line(3)
The "broken line" glyph
Bio::Graphics::Glyph::cds(3)
The "cds" glyph
Bio::Graphics::Glyph::christmas_arrow(3)
The "christmas arrow" glyph
Bio::Graphics::Glyph::crossbox(3)
The "crossbox" glyph
Bio::Graphics::Glyph::dashed_line(3)
The "dashed line" glyph
Bio::Graphics::Glyph::decorated_gene(3)
A GFF3-compatible gene glyph with protein decorations
Bio::Graphics::Glyph::decorated_transcript(3)
draws processed transcript with protein decorations
Bio::Graphics::Glyph::diamond(3)
The "diamond" glyph
Bio::Graphics::Glyph::dna(3)
The "dna" glyph
Bio::Graphics::Glyph::dot(3)
The "dot" glyph
Bio::Graphics::Glyph::dumbbell(3)
A glyph that draws a "dumbbell" with the same shapes on both ends
Bio::Graphics::Glyph::ellipse(3)
The "ellipse" glyph
Bio::Graphics::Glyph::ex(3)
the "ex", or "crossed box" glyph
Bio::Graphics::Glyph::extending_arrow(3)
-- The "extending arrow" glyph
Bio::Graphics::Glyph::fixedwidth(3)
A base class fixed width glyphs
Bio::Graphics::Glyph::flag(3)
the "flag" glyph
Bio::Graphics::Glyph::gene(3)
A GFF3-compatible gene glyph
Bio::Graphics::Glyph::generic(3)
The "generic" glyph
Bio::Graphics::Glyph::graded_segments(3)
The "graded_segments" glyph
Bio::Graphics::Glyph::group(3)
The "group" glyph
Bio::Graphics::Glyph::hat(3)
The "hat" glyph
Bio::Graphics::Glyph::heat_map(3)
The "heat_map" glyph
Bio::Graphics::Glyph::heat_map_ideogram(3)
The "heat_map_ideogram" glyph
Bio::Graphics::Glyph::heterogeneous_segments(3)
The "heterogeneous_segments" glyph
Bio::Graphics::Glyph::hidden(3)
The "hidden" glyph
Bio::Graphics::Glyph::hybrid_plot(3)
An xyplot plot drawing dual graph using data from two or more wiggle files per track
Bio::Graphics::Glyph::ideogram(3)
The "ideogram" glyph
Bio::Graphics::Glyph::image(3)
A glyph that draws photographs & other images
Bio::Graphics::Glyph::lightning(3)
The "lightning" glyph
Bio::Graphics::Glyph::line(3)
The "line" glyph
Bio::Graphics::Glyph::merge_parts(3)
a base class which suppors semantic zooming of scored alignment features
Bio::Graphics::Glyph::merged_alignment(3)
The "merged_alignment" glyph
Bio::Graphics::Glyph::minmax(3)
The minmax glyph
Bio::Graphics::Glyph::operon(3)
The "polycistronic operon" glyph
Bio::Graphics::Glyph::oval(3)
The "oval" glyph
Bio::Graphics::Glyph::pairplot(3)
The "pairwise plot" glyph
Bio::Graphics::Glyph::pentagram(3)
The "pentagram" glyph
Bio::Graphics::Glyph::phylo_align(3)
The "phylogenetic alignment" glyph
Bio::Graphics::Glyph::pinsertion(3)
The "Drosophila P-element Insertion" glyph
Bio::Graphics::Glyph::primers(3)
The "STS primers" glyph
Bio::Graphics::Glyph::processed_transcript(3)
The sequence ontology transcript glyph
Bio::Graphics::Glyph::protein(3)
The "protein" glyph
Bio::Graphics::Glyph::ragged_ends(3)
The "ragged ends" glyph
Bio::Graphics::Glyph::redgreen_box(3)
The "redgreen_box" glyph
Bio::Graphics::Glyph::redgreen_segment(3)
The "redgreen_segments" glyph
Bio::Graphics::Glyph::repeating_shape(3)
A glyph that draws the same shape repeatedly
Bio::Graphics::Glyph::rndrect(3)
The "round rect" glyph
Bio::Graphics::Glyph::ruler_arrow(3)
glyph for drawing an arrow as ruler (5' and 3' are marked as label)
Bio::Graphics::Glyph::saw_teeth(3)
The "saw teeth" glyph
Bio::Graphics::Glyph::scale(3)
The "scale" glyph
Bio::Graphics::Glyph::segmented_keyglyph(3)
The "segmented_keyglyph" glyph
Bio::Graphics::Glyph::segments(3)
The "segments" glyph
Bio::Graphics::Glyph::so_transcript(3)
The sequence ontology transcript glyph
Bio::Graphics::Glyph::span(3)
The "span" glyph
Bio::Graphics::Glyph::spectrogram(3)
The "spectrogram" glyph
Bio::Graphics::Glyph::splice_site(3)
The "splice_site" glyph
Bio::Graphics::Glyph::stackedplot(3)
The stackedplot glyph
Bio::Graphics::Glyph::ternary_plot(3)
Draw ternary plot data
Bio::Graphics::Glyph::text_in_box(3)
The "text in box" glyph
Bio::Graphics::Glyph::three_letters(3)
DAS-compatible package to use for drawing a line of groups of three letters
Bio::Graphics::Glyph::tic_tac_toe(3)
The "tic-tac-toe" glyph
Bio::Graphics::Glyph::toomany(3)
The "too many to show" glyph
Bio::Graphics::Glyph::trace(3)
A glyph that visualizes a trace file
Bio::Graphics::Glyph::track(3)
The "track" glyph
Bio::Graphics::Glyph::transcript(3)
The "transcript" glyph
Bio::Graphics::Glyph::transcript2(3)
The "transcript2" glyph
Bio::Graphics::Glyph::translation(3)
The "6-frame translation" glyph
Bio::Graphics::Glyph::triangle(3)
The "triangle" glyph
Bio::Graphics::Glyph::two_bolts(3)
The "two bolts" glyph
Bio::Graphics::Glyph::vista_plot(3)
The "vista_plot" glyph
Bio::Graphics::Glyph::wave(3)
The "wave" glyph
Bio::Graphics::Glyph::weighted_arrow(3)
The "weighted arrow" glyph
Bio::Graphics::Glyph::whiskerplot(3)
The whiskerplot glyph
Bio::Graphics::Glyph::wiggle_box(3)
A generic box glyph compatible with dense "wig"data
Bio::Graphics::Glyph::wiggle_density(3)
A density plot compatible with dense "wig"data
Bio::Graphics::Glyph::wiggle_xyplot(3)
An xyplot plot compatible with dense "wig"data
Bio::Graphics::Glyph::xyplot(3)
The xyplot glyph
Bio::Graphics::Panel(3)
Generate GD images of Bio::Seq objects
Bio::Graphics::Pictogram(3)
generate SVG output of Pictogram display for consensus motifs
Bio::Graphics::RendererI(3)
A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI
Bio::Graphics::Util(3)
non-object-oriented utilities used in Bio::Graphics modules "($frame,$offset) = frame_and_offset($pos,$strand,$phase)" 4 Item "($frame,$offset) = frame_and_offset($pos,$strand,$phase)" Calculate the reading frame for a given genomic position, strand and phase. The offset is the offset from $pos to the first nucleotide of the reading frame. In a scalar context, returns the frame only
Bio::Graphics::Wiggle(3)
-- Binary storage for dense genomic features
Bio::HandlerBaseI(3)
Interface class for handler methods which interact with any event-driven parsers (drivers)
Bio::IdCollectionI(3)
interface for objects with multiple identifiers
Bio::IdentifiableI(3)
interface for objects with identifiers
Bio::Index::Abstract(3)
Abstract interface for indexing a flat file
Bio::Index::AbstractSeq(3)
base class for AbstractSeq
Bio::Index::Blast(3)
Indexes Blast reports and supports retrieval based on query accession(s)
Bio::Index::BlastTable(3)
Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
Bio::Index::EMBL(3)
Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format)
Bio::Index::Fasta(3)
Interface for indexing (multiple) fasta files
Bio::Index::Fastq(3)
Interface for indexing (multiple) fastq files
Bio::Index::GenBank(3)
Interface for indexing one or more GenBank files (i.e. flat file GenBank format)
Bio::Index::Qual(3)
Interface for indexing (multiple) fasta qual files
Bio::Index::SwissPfam(3)
Interface for indexing swisspfam files
Bio::Index::Swissprot(3)
Interface for indexing one or more Swissprot files
Bio::LocatableSeq(3)
A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq
Bio::Location::Atomic(3)
Implementation of a Atomic Location on a Sequence
Bio::Location::AvWithinCoordPolicy(3)
class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Bio::Location::CoordinatePolicyI(3)
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Bio::Location::Fuzzy(3)
Implementation of a Location on a Sequence which has unclear start and/or end locations
Bio::Location::FuzzyLocationI(3)
Abstract interface of a Location on a Sequence which has unclear start/end location
Bio::Location::NarrowestCoordPolicy(3)
class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Bio::Location::Simple(3)
Implementation of a Simple Location on a Sequence
Bio::Location::Split(3)
Implementation of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::SplitLocationI(3)
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::WidestCoordPolicy(3)
class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Bio::LocationI(3)
Abstract interface of a Location on a Sequence
Bio::MAGETAB(3)
A data model and utility API for the MAGE-TAB format
Bio::MAGETAB::ArrayDesign(3)
MAGE-TAB array design class
Bio::MAGETAB::Assay(3)
MAGE-TAB assay class
Bio::MAGETAB::BaseClass(3)
Abstract base class for all MAGE-TAB classes
Bio::MAGETAB::Comment(3)
MAGE-TAB user-defined comment class
Bio::MAGETAB::CompositeElement(3)
MAGE-TAB composite element class
Bio::MAGETAB::Contact(3)
MAGE-TAB contact class
Bio::MAGETAB::ControlledTerm(3)
MAGE-TAB controlled term class
Bio::MAGETAB::Data(3)
Abstract data class
Bio::MAGETAB::DataAcquisition(3)
MAGE-TAB data acquisition class
Bio::MAGETAB::DataFile(3)
MAGE-TAB data file class
Bio::MAGETAB::DataMatrix(3)
MAGE-TAB data matrix class
Bio::MAGETAB::DatabaseEntry(3)
MAGE-TAB database entry class
Bio::MAGETAB::DesignElement(3)
Abstract design element class
Bio::MAGETAB::Edge(3)
MAGE-TAB edge class
Bio::MAGETAB::Event(3)
Abstract event class
Bio::MAGETAB::Extract(3)
MAGE-TAB extract class
Bio::MAGETAB::Factor(3)
MAGE-TAB experimental factor class
Bio::MAGETAB::FactorValue(3)
MAGE-TAB experimental factor class
Bio::MAGETAB::Feature(3)
MAGE-TAB feature class
Bio::MAGETAB::Investigation(3)
MAGE-TAB investigation class
Bio::MAGETAB::LabeledExtract(3)
MAGE-TAB labeled extract class
Bio::MAGETAB::Material(3)
Abstract material class
Bio::MAGETAB::MatrixColumn(3)
MAGE-TAB matrix column class
Bio::MAGETAB::MatrixRow(3)
MAGE-TAB matrix row class
Bio::MAGETAB::Measurement(3)
MAGE-TAB measurement class
Bio::MAGETAB::Node(3)
Abstract node class
Bio::MAGETAB::Normalization(3)
MAGE-TAB data acquisition class
Bio::MAGETAB::ParameterValue(3)
MAGE-TAB parameter value class
Bio::MAGETAB::Protocol(3)
MAGE-TAB protocol class
Bio::MAGETAB::ProtocolApplication(3)
MAGE-TAB protocol application class
Bio::MAGETAB::ProtocolParameter(3)
MAGE-TAB protocol parameter class
Bio::MAGETAB::Publication(3)
MAGE-TAB publication class
Bio::MAGETAB::Reporter(3)
MAGE-TAB reporter class
Bio::MAGETAB::SDRF(3)
MAGE-TAB SDRF class
Bio::MAGETAB::SDRFRow(3)
MAGE-TAB SDRF row class
Bio::MAGETAB::Sample(3)
MAGE-TAB sample class
Bio::MAGETAB::Source(3)
MAGE-TAB source class
Bio::MAGETAB::TermSource(3)
MAGE-TAB term source class
Bio::MAGETAB::Types(3)
custom data types for Bio::MAGETAB
Bio::MAGETAB::Util::Builder(3)
A storage class used to track Bio::MAGETAB object creation
Bio::MAGETAB::Util::DBLoader(3)
A persistent storage class used to track Bio::MAGETAB object creation and insertion into a relational database
Bio::MAGETAB::Util::Persistence(3)
A Tangram-based object persistence class for MAGE-TAB
Bio::MAGETAB::Util::Reader(3)
A parser/validator for MAGE-TAB documents
Bio::MAGETAB::Util::Reader::ADF(3)
ADF parser class
Bio::MAGETAB::Util::Reader::DataMatrix(3)
Data matrix parser class
Bio::MAGETAB::Util::Reader::IDF(3)
IDF parser class
Bio::MAGETAB::Util::Reader::SDRF(3)
SDRF parser class
Bio::MAGETAB::Util::Reader::Tabfile(3)
An abstract class providing methods for handling tab-delimited files
Bio::MAGETAB::Util::Reader::TagValueFile(3)
An abstract class providing methods for handling tab-delimited files
Bio::MAGETAB::Util::RewriteAE(3)
A utility class providing methods to correct some common errors in ArrayExpress MAGE-TAB documents
Bio::MAGETAB::Util::Writer(3)
Export of MAGE-TAB objects
Bio::MAGETAB::Util::Writer::ADF(3)
Export of MAGE-TAB ArrayDesign objects
Bio::MAGETAB::Util::Writer::GraphViz(3)
Visualization of MAGE-TAB objects
Bio::MAGETAB::Util::Writer::IDF(3)
Export of MAGE-TAB Investigation objects
Bio::MAGETAB::Util::Writer::SDRF(3)
Export of MAGE-TAB SDRF objects
Bio::MAGETAB::Util::Writer::Tabfile(3)
Abstract MAGE-TAB exporter class
Bio::Matrix::Generic(3)
A generic matrix implementation
Bio::Matrix::IO(3)
A factory for Matrix parsing
Bio::Matrix::IO::mlagan(3)
A parser for the mlagan substitution matrix
Bio::Matrix::IO::phylip(3)
A parser for PHYLIP distance matricies
Bio::Matrix::IO::scoring(3)
A parser for PAM/BLOSUM matricies
Bio::Matrix::MatrixI(3)
An interface for describing a Matrix
Bio::Matrix::Mlagan(3)
A generic matrix with mlagan fields
Bio::Matrix::PSM::IO(3)
PSM parser
Bio::Matrix::PSM::IO::mast(3)
PSM mast parser implementation
Bio::Matrix::PSM::IO::masta(3)
motif fasta format parser
Bio::Matrix::PSM::IO::meme(3)
PSM meme parser implementation
Bio::Matrix::PSM::IO::psiblast(3)
PSM psiblast parser
Bio::Matrix::PSM::IO::transfac(3)
PSM transfac parser
Bio::Matrix::PSM::InstanceSite(3)
A PSM site occurrence
Bio::Matrix::PSM::InstanceSiteI(3)
InstanceSite interface, holds an instance of a PSM
Bio::Matrix::PSM::ProtMatrix(3)
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information
Bio::Matrix::PSM::ProtPsm(3)
handle combination of site matricies
Bio::Matrix::PSM::Psm(3)
handle combination of site matricies
Bio::Matrix::PSM::PsmHeader(3)
PSM mast parser implementation
Bio::Matrix::PSM::PsmHeaderI(3)
handles the header data from a PSM file
Bio::Matrix::PSM::PsmI(3)
abstract interface to handler of site matricies
Bio::Matrix::PSM::SiteMatrix(3)
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
Bio::Matrix::PSM::SiteMatrixI(3)
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
Bio::Matrix::PhylipDist(3)
A Phylip Distance Matrix object
Bio::Matrix::Scoring(3)
Object which can hold scoring matrix information
Bio::NEXUS(3)
An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
Bio::NEXUS::AssumptionsBlock(3)
Represents ASSUMPTIONS block of a NEXUS file
Bio::NEXUS::Block(3)
Provides useful functions for blocks in NEXUS file (parent class)
Bio::NEXUS::CharactersBlock(3)
Represents a CHARACTERS Block (Data or Characters) of a NEXUS file
Bio::NEXUS::CodonsBlock(3)
Represents CODONS block in NEXUS file
Bio::NEXUS::DataBlock(3)
Represents the deprecated DATA Block in NEXUS file
Bio::NEXUS::DistancesBlock(3)
Represents DISTANCES block in NEXUS file
Bio::NEXUS::Functions(3)
Provides private utiliy functions for the module
Bio::NEXUS::HistoryBlock(3)
Represents a HISTORY block of a NEXUS file
Bio::NEXUS::Matrix(3)
Provides functions for handling blocks that have matrices
Bio::NEXUS::NHXCmd(3)
Provides functions for manipulating nodes in trees
Bio::NEXUS::Node(3)
Provides functions for manipulating nodes in trees
Bio::NEXUS::NotesBlock(3)
Represents a NOTES block in a NEXUS file
Bio::NEXUS::SetsBlock(3)
Represents SETS block of a NEXUS file
Bio::NEXUS::SpanBlock(3)
Represent SPAN block in a NEXUS file (contains meta data)
Bio::NEXUS::TaxUnit(3)
Represents a taxon unit in a NEXUS file
Bio::NEXUS::TaxUnitSet(3)
Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file
Bio::NEXUS::TaxaBlock(3)
Represents TAXA block of a NEXUS file
Bio::NEXUS::Tools::GraphicsParams(3), Graphics(3)
represents a character block (Data or Characters) of a NEXUS file
Bio::NEXUS::Tools::NexModifier(3), Bio::NEXUS::Tools::Modifier(3)
NEXUS file content modifier ( exclude/select/rename options on OTUs)
Bio::NEXUS::Tools::NexPlotter(3), nexplot.pl(3)
PostScript plot of tree + data table (from NEXUS infile) =head1 SYNOPSIS nexplot.pl [options] foo.nex [tree_name] > foo.ps =head1 OPTIONS -h Brief help message -d Full documentation -v Verbose mode -V Print version information and quit -f Specify output file (default: STDOUT) INFORMATION TO DISPLAY -b Turn on bootstrap values, if any -i Turn on internal node labeling -t Tree only (ignore any characters) -I Specify character block (by "Title") to be used in matrix (e.g. "dna", "protein", "intron") -m Matrix only (ignore any trees) -c Cladogram mode: (auto if no branch lengths present in tree) normal: all branch lengths equal accelerated: same as normal except OTUs are aligned at end -U Display taxa sets in color (-U "set1 color1 [set2 color2 ...]") Color options are red, orange, green, forest, aqua, blue, purple, pink, brown, gray, black PLOT FORMATTING -r Right-justify labels (default: left-justified) -C Columns of characters per block (default = 10) -T Specify tree width (longest branch; default: 10") -S Spacing (vertically) between OTUs (default: .25") -R Ratio of font height to Spacing (default: 0.8; rec: 0.5-1) -F Font to use for labels and titles -B Draw a box indicating postscriptes bounds of the plot area -g Include gray lines after OTU labels, even if -t (tree only) option is used PAGE SETUP -s Print on multiple pages, but shrink to page height -o Print on multiple pages at actual size -W Specify output page width (default: 8.5") -H Specify output page height (default: 11") -a Change page dimensions to fit plot =head1 DESCRIPTION B<This program> will read a NEXUS file and output a PostScript display of trees (one file for each tree in the tree block), as well as any character matrix (e.g. sequences) if present in the file. =head1 FILES =over 4 =back =head1 VERSION $Id: NexPlotter.pm,v 1.2 2008/06/16 19:53:41 astoltzfus Exp $
Bio::NEXUS::Tree(3)
Provides functions for manipulating trees
Bio::NEXUS::TreesBlock(3)
Represents TREES block of a NEXUS file
Bio::NEXUS::UnalignedBlock(3)
Represents an UNALIGNED block of a NEXUS file
Bio::NEXUS::UnknownBlock(3)
Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module
Bio::NEXUS::Util::Exceptions(3)
Exception classes for Bio::NEXUS
Bio::NEXUS::Util::Logger(3)
Logging for Bio::NEXUS
Bio::NEXUS::WeightSet(3)
Represents column weights in alignment ( for each character)
Bio::Ontology::DocumentRegistry(3)
Keep track of where to find ontologies. Allows lookups by name
Bio::Ontology::GOterm(3)
representation of GO terms
Bio::Ontology::InterProTerm(3)
Implementation of InterProI term interface
Bio::Ontology::OBOEngine(3)
An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
Bio::Ontology::OBOterm(3)
representation of OBO terms
Bio::Ontology::Ontology(3)
standard implementation of an Ontology
Bio::Ontology::OntologyEngineI(3)
Interface a minimal Ontology implementation should satisfy
Bio::Ontology::OntologyI(3)
Interface for an ontology implementation
Bio::Ontology::OntologyStore(3)
A repository of ontologies
Bio::Ontology::Path(3)
a path for an ontology term graph
Bio::Ontology::PathI(3)
Interface for a path between ontology terms
Bio::Ontology::Relationship(3)
a relationship for an ontology
Bio::Ontology::RelationshipFactory(3)
Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
Bio::Ontology::RelationshipI(3)
Interface for a relationship between ontology terms
Bio::Ontology::RelationshipType(3), Bio::Ontology::RelationshipType (3)
a relationship type for an ontology
Bio::Ontology::SimpleGOEngine::GraphAdaptor(3)
Graph adaptor for Bio::Ontology::SimpleGOEngine
Bio::Ontology::SimpleOntologyEngine(3)
Implementation of OntologyEngineI interface
Bio::Ontology::Term(3)
implementation of the interface for ontology terms
Bio::Ontology::TermFactory(3)
Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
Bio::Ontology::TermI(3)
interface for ontology terms
Bio::OntologyIO(3)
Parser factory for Ontology formats
Bio::OntologyIO::Handlers::BaseSAXHandler(3)
base class for SAX Handlers
Bio::OntologyIO::Handlers::InterProHandler(3)
XML handler class for InterProParser
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3)
parse an InterPro XML file and persist the resulting terms to a Biosql database
Bio::OntologyIO::InterProParser(3)
Parser for InterPro xml files
Bio::OntologyIO::dagflat(3)
a base class parser for GO flat-file type formats
Bio::OntologyIO::goflat(3)
a parser for the Gene Ontology flat-file format
Bio::OntologyIO::obo(3)
parser for OBO flat-file format
Bio::OntologyIO::simplehierarchy(3)
a base class parser for simple hierarchy-by-indentation type formats
Bio::OntologyIO::soflat(3)
a parser for the Sequence Ontology flat-file format
Bio::ParameterBaseI(3)
Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends
Bio::Phylo(3)
Phylogenetic analysis using perl
Bio::Phylo::EvolutionaryModels(3)
Evolutionary models for phylogenetic trees and methods to sample these Klaas Hartmann, September 2007
Bio::Phylo::Factory(3)
Creator of objects, reduces hardcoded class names in code
Bio::Phylo::Forest(3)
Container for tree objects
Bio::Phylo::Forest::DrawNodeRole(3)
Tree node with extra methods for tree drawing
Bio::Phylo::Forest::DrawTreeRole(3)
Tree with extra methods for tree drawing
Bio::Phylo::Forest::Node(3)
Node in a phylogenetic tree
Bio::Phylo::Forest::NodeRole(3)
Extra behaviours for a node in a phylogenetic tree
Bio::Phylo::Forest::Tree(3)
Phylogenetic tree
Bio::Phylo::Forest::TreeRole(3)
Extra behaviours for a phylogenetic tree
Bio::Phylo::Generator(3)
Generator of tree topologies
Bio::Phylo::IO(3)
Front end for parsers and serializers
Bio::Phylo::Identifiable(3)
Objects with unique identifiers
Bio::Phylo::Listable(3)
List of things, super class for many objects
Bio::Phylo::ListableRole(3)
Extra functionality for things that are lists
Bio::Phylo::Manual(3)
High-level user guide
Bio::Phylo::Matrices(3)
Container of matrix objects
Bio::Phylo::Matrices::Character(3)
A character (column) in a matrix
Bio::Phylo::Matrices::Characters(3)
Container of character objects
Bio::Phylo::Matrices::Datatype(3)
Validator of character state data
Bio::Phylo::Matrices::Datatype::Continuous(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Custom(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Dna(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Illumina(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Mixed(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Protein(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Restriction(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Rna(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Sanger(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Solexa(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datatype::Standard(3)
Validator subclass, no serviceable parts inside
Bio::Phylo::Matrices::Datum(3)
Character state sequence
Bio::Phylo::Matrices::DatumRole(3)
Extra behaviours for a character state sequence
Bio::Phylo::Matrices::Matrix(3)
Character state matrix
Bio::Phylo::Matrices::MatrixRole(3)
Extra behaviours for a character state matrix
Bio::Phylo::Matrices::TypeSafeData(3)
Superclass for objects that contain character data
Bio::Phylo::Mediators::TaxaMediator(3)
Mediator for links between taxa and other objects
Bio::Phylo::Models::Substitution::Binary(3)
Binary character substitution model
Bio::Phylo::Models::Substitution::Dna(3)
DNA substitution model
Bio::Phylo::Models::Substitution::Dna::F81(3)
Felsenstein (1981) model
Bio::Phylo::Models::Substitution::Dna::GTR(3)
General Time Reversible model
Bio::Phylo::Models::Substitution::Dna::HKY85(3)
Hasegawa, Kishino, Yano (1985) model
Bio::Phylo::Models::Substitution::Dna::JC69(3)
Jukes, Cantor (1969)
Bio::Phylo::Models::Substitution::Dna::K80(3)
Kimura 2-parameter
Bio::Phylo::NeXML::DOM(3)
XML DOM support for Bio::Phylo
Bio::Phylo::NeXML::DOM::Document(3)
XML DOM Abstract class for flexible document object model implementation
Bio::Phylo::NeXML::DOM::Document::Libxml(3)
XML DOM document mappings to the "XML::LibXML" package
Bio::Phylo::NeXML::DOM::Document::Twig(3)
XML DOM document mappings to the "XML::Twig" package
Bio::Phylo::NeXML::DOM::Element(3)
XML DOM Abstract class for flexible document object model implementation
Bio::Phylo::NeXML::DOM::Element::Libxml(3)
XML DOM element mappings to the "XML::LibXML" package
Bio::Phylo::NeXML::DOM::Element::Twig(3)
XML DOM mappings to the XML::Twig package
Bio::Phylo::NeXML::Entities(3)
Functions for dealing with XML entities
Bio::Phylo::NeXML::Meta(3)
Single predicate/object annotation, attached to an xml-writable subject
Bio::Phylo::NeXML::Meta::XMLLiteral(3)
Annotation value adaptor, no direct usage
Bio::Phylo::NeXML::Writable(3)
Superclass for objects that serialize to NeXML
Bio::Phylo::NeXML::XML2JSON(3)
Helps convert NeXML to JSON, no serviceable parts inside
Bio::Phylo::Parsers::Abstract(3)
Superclass for parsers used by Bio::Phylo::IO
Bio::Phylo::Parsers::Adjacency(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Cdao(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Dwca(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Fasta(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Fastq(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Figtree(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Json(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Newick(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Nexml(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Nexus(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Nhx(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Phylip(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Phyloxml(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Table(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Taxlist(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Tnrs(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Tolweb(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Ubiocbmeta(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Ubiometa(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Parsers::Ubiosearch(3)
Parser used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::PhyloWS(3)
Base class for phylogenetic web services
Bio::Phylo::PhyloWS::Client(3)
Base class for phylogenetic web service clients
Bio::Phylo::PhyloWS::Resource(3)
Represents a PhyloWS web resource
Bio::Phylo::PhyloWS::Resource::Description(3)
Represents a PhyloWS resource description
Bio::Phylo::PhyloWS::Service(3)
Base class for phylogenetic web services
Bio::Phylo::PhyloWS::Service::Timetree(3)
PhyloWS service wrapper for Timetree
Bio::Phylo::PhyloWS::Service::Tolweb(3)
PhyloWS service wrapper for Tree of Life
Bio::Phylo::PhyloWS::Service::UbioClassificationBank(3)
PhyloWS service wrapper for uBio ClassificationBank records
Bio::Phylo::PhyloWS::Service::UbioNameBank(3)
PhyloWS service wrapper for uBio NameBank records
Bio::Phylo::Project(3)
Container for related data
Bio::Phylo::Set(3)
Subset of the parts inside a container
Bio::Phylo::Taxa(3)
Container of taxon objects
Bio::Phylo::Taxa::TaxaLinker(3)
Superclass for objects that link to taxa objects
Bio::Phylo::Taxa::Taxon(3)
Operational taxonomic unit
Bio::Phylo::Taxa::TaxonLinker(3)
Superclass for objects that link to taxon objects
Bio::Phylo::Treedrawer(3)
Visualizer of tree shapes
Bio::Phylo::Treedrawer::Abstract(3)
Abstract graphics writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Canvas(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Gif(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Jpeg(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Pdf(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Png(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Processing(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Svg(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Treedrawer::Swf(3)
Graphics format writer used by treedrawer, no serviceable parts inside
Bio::Phylo::Unparsers::Abstract(3)
Superclass for unparsers used by Bio::Phylo::IO
Bio::Phylo::Unparsers::Adjacency(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Cdao(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Fasta(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Figtree(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Hennig86(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Html(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Json(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Mrp(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Newick(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Nexml(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Nexus(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Nhx(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Nwmsrdf(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Pagel(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Phylip(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Phyloxml(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Rss1(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Unparsers::Taxlist(3)
Serializer used by Bio::Phylo::IO, no serviceable parts inside
Bio::Phylo::Util::CONSTANT(3)
Global constants and utility functions
Bio::Phylo::Util::CONSTANT::Int(3)
Integer constants, no serviceable parts inside
Bio::Phylo::Util::Dependency(3)
Utility class for importing external dependencies. No serviceable parts inside
Bio::Phylo::Util::Exceptions(3)
Errors ($@) that are objects
Bio::Phylo::Util::IDPool(3)
Utility class for generating object IDs. No serviceable parts inside
Bio::Phylo::Util::Logger(3)
Logger of internal messages of several severity levels
Bio::Phylo::Util::MOP(3)
Meta-object programming, no serviceable parts inside
Bio::Phylo::Util::Math(3)
Utility math functions
Bio::Phylo::Util::OptionalInterface(3)
Utility class for managing optional superclasses. No serviceable parts inside
Bio::Phylo::Util::StackTrace(3)
Stack traces for exceptions
Bio::PhyloRole(3)
Extra behaviours for the base class
Bio::PrimarySeq(3)
Bioperl lightweight sequence object
Bio::PrimarySeqI(3)
Interface definition for a Bio::PrimarySeq
Bio::PullParserI(3)
A base module for fast 'pull' parsing
Bio::Range(3)
Pure perl RangeI implementation
Bio::RangeI(3)
Range interface
Bio::Root::Exception(3)
BioPerl exceptions
Bio::Root::HTTPget(3)
module for fallback HTTP get operations when LWP:: is unavailable
Bio::Root::IO(3)
BioPerl base IO handling class
Bio::Root::Root(3)
implementation of Bio::Root::RootI interface
Bio::Root::RootI(3)
base interface for all BioPerl classes
Bio::Root::Storable(3)
Safely store/retrieve objects from disk
Bio::Root::Test(3)
common base for all BioPerl test scripts
Bio::Root::TestObject(3), TestObject(3)
An implementation of TestInterface
Bio::Root::Utilities(3)
general-purpose utilities
Bio::Root::Version(3)
don't use, get version from each module
Bio::SCF(3)
Perl extension for reading and writting SCF sequence files
Bio::Search::BlastStatistics(3)
An object for Blast statistics
Bio::Search::BlastUtils(3)
Utility functions for Bio::Search:: BLAST objects
Bio::Search::DatabaseI(3)
Interface for a database used in a sequence search
Bio::Search::GenericDatabase(3)
Generic implementation of Bio::Search::DatabaseI
Bio::Search::GenericStatistics(3)
An object for statistics
Bio::Search::HSP::BlastHSP(3)
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::BlastPullHSP(3)
A parser and HSP object for BlastN hsps
Bio::Search::HSP::FastaHSP(3)
HSP object for FASTA specific data
Bio::Search::HSP::GenericHSP(3)
A "Generic" implementation of a High Scoring Pair
Bio::Search::HSP::HSPFactory(3)
A factory to create Bio::Search::HSP::HSPI objects
Bio::Search::HSP::HSPI(3)
Interface for a High Scoring Pair in a similarity search result
Bio::Search::HSP::ModelHSP(3)
A HSP object for model-based searches
Bio::Search::HSP::PSLHSP(3)
A HSP for PSL output
Bio::Search::HSP::PsiBlastHSP(3)
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::PullHSPI(3)
Bio::Search::HSP::HSPI interface for pull parsers
Bio::Search::HSP::WABAHSP(3)
HSP object suitable for describing WABA alignments
Bio::Search::Hit::BlastHit(3)
Blast-specific subclass of Bio::Search::Hit::GenericHit
Bio::Search::Hit::BlastPullHit(3)
A parser and hit object for BLASTN hits
Bio::Search::Hit::Fasta(3)
Hit object specific for Fasta-generated hits
Bio::Search::Hit::GenericHit(3)
A generic implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::HitFactory(3)
A factory to create Bio::Search::Hit::HitI objects
Bio::Search::Hit::HitI(3)
Interface for a hit in a similarity search result
Bio::Search::Hit::ModelHit(3)
A model-based implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::PsiBlastHit(3)
Bioperl BLAST Hit object
Bio::Search::Hit::PullHitI(3)
Bio::Search::Hit::HitI interface for pull parsers
Bio::Search::Iteration::GenericIteration(3)
A generic implementation of the Bio::Search::Iteration::IterationI interface
Bio::Search::Iteration::IterationI(3)
Abstract interface to an iteration from an iterated search result, such as PSI-BLAST
Bio::Search::Processor(3)
DESCRIPTION of Object
Bio::Search::Result::BlastPullResult(3)
A parser and result object for BLASTN results
Bio::Search::Result::BlastResult(3)
Blast-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::CrossMatchResult(3)
CrossMatch-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::GenericResult(3)
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results
Bio::Search::Result::INFERNALResult(3)
A Result object for INFERNAL results
Bio::Search::Result::PullResultI(3)
Bio::Search::Result::ResultI interface for 'pull' parsers
Bio::Search::Result::ResultFactory(3)
A factory to create Bio::Search::Result::ResultI objects
Bio::Search::Result::ResultI(3)
Abstract interface to Search Result objects
Bio::Search::Result::WABAResult(3)
Result object for WABA alignment output
Bio::Search::SearchUtils(3)
Utility functions for Bio::Search:: objects
Bio::Search::StatisticsI(3)
A Base object for statistics
Bio::Search::Tiling::MapTileUtils(3)
utilities for manipulating closed intervals for an HSP tiling algorithm
Bio::Search::Tiling::MapTiling(3)
An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
Bio::Search::Tiling::TilingI(3)
Abstract interface for an HSP tiling module
Bio::SearchIO(3)
Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
Bio::SearchIO::EventHandlerI(3)
An abstract Event Handler for Search Result parsing
Bio::SearchIO::FastHitEventBuilder(3)
Event Handler for SearchIO events
Bio::SearchIO::IteratedSearchResultEventBuilder(3)
Event Handler for SearchIO events
Bio::SearchIO::SearchResultEventBuilder(3)
Event Handler for SearchIO events
Bio::SearchIO::SearchWriterI(3)
Interface for outputting parsed Search results
Bio::SearchIO::Writer::GbrowseGFF(3)
Interface for outputting parsed search results in Gbrowse GFF format
Bio::SearchIO::Writer::HSPTableWriter(3)
Tab-delimited data for Bio::Search::HSP::HSPI objects
Bio::SearchIO::Writer::HTMLResultWriter(3)
write a Bio::Search::ResultI in HTML
Bio::SearchIO::Writer::HitTableWriter(3)
Tab-delimited data for Bio::Search::Hit::HitI objects
Bio::SearchIO::Writer::ResultTableWriter(3)
Outputs tab-delimited data for each Bio::Search::Result::ResultI object
Bio::SearchIO::Writer::TextResultWriter(3)
Object to implement writing a Bio::Search::ResultI in Text
Bio::SearchIO::axt(3)
a parser for axt format reports
Bio::SearchIO::blast(3)
Event generator for event based parsing of blast reports
Bio::SearchIO::blast_pull(3)
A parser for BLAST output
Bio::SearchIO::blasttable(3)
Driver module for SearchIO for parsing NCBI -m 8/9 format
Bio::SearchIO::cross_match(3)
CrossMatch-specific subclass of Bio::SearchIO
Bio::SearchIO::erpin(3)
SearchIO-based ERPIN parser
Bio::SearchIO::exonerate(3)
parser for Exonerate
Bio::SearchIO::fasta(3)
A SearchIO parser for FASTA results
Bio::SearchIO::gmap_f9(3)
Event generator for parsing gmap reports (Z format)
Bio::SearchIO::infernal(3)
SearchIO-based Infernal parser
Bio::SearchIO::megablast(3)
a driver module for Bio::SearchIO to parse megablast reports (format 0)
Bio::SearchIO::psl(3)
A parser for PSL output (UCSC)
Bio::SearchIO::rnamotif(3)
SearchIO-based RNAMotif parser
Bio::SearchIO::sim4(3)
parser for Sim4 alignments
Bio::SearchIO::waba(3)
SearchIO parser for Jim Kent WABA program alignment output
Bio::SearchIO::wise(3)
Parsing of wise output as alignments
Bio::Seq(3)
Sequence object, with features
Bio::Seq::BaseSeqProcessor(3)
Base implementation for a SequenceProcessor
Bio::Seq::EncodedSeq(3)
subtype of Bio::LocatableSeq to store DNA that encodes a protein
Bio::Seq::LargeLocatableSeq(3)
LocatableSeq object that stores sequence as files in the tempdir
Bio::Seq::LargePrimarySeq(3)
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root
Bio::Seq::LargeSeq(3)
SeqI compliant object that stores sequence as files in /tmp
Bio::Seq::LargeSeqI(3)
Interface class for sequences that cache their residues in a temporary file
Bio::Seq::Meta(3)
Generic superclass for sequence objects with residue-based meta information
Bio::Seq::Meta::Array(3)
array-based generic implementation of a sequence class with residue-based meta information
Bio::Seq::MetaI(3)
Interface for sequence objects with residue-based meta information
Bio::Seq::PrimaryQual(3)
Bioperl lightweight Quality Object
Bio::Seq::PrimedSeq(3)
A sequence and a pair of primers matching on it
Bio::Seq::QualI(3)
Interface definition for a Bio::Seq::Qual
Bio::Seq::Quality(3)
Implementation of sequence with residue quality and trace values
Bio::Seq::RichSeq(3)
Module implementing a sequence created from a rich sequence database entry
Bio::Seq::RichSeqI(3)
interface for sequences from rich data sources, mostly databases
Bio::Seq::SeqBuilder(3)
Configurable object builder for sequence stream parsers
Bio::Seq::SeqFactory(3)
Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory
Bio::Seq::SeqFastaSpeedFactory(3)
Rapid creation of Bio::Seq objects through a factory
Bio::Seq::SequenceTrace(3)
Bioperl object packaging a sequence with its trace
Bio::Seq::SimulatedRead(3)
Read with sequencing errors taken from a reference sequence
Bio::Seq::TraceI(3)
Interface definition for a Bio::Seq::Trace
Bio::SeqAnalysisParserI(3)
Sequence analysis output parser interface
Bio::SeqFeature::Amplicon(3)
Amplicon feature
Bio::SeqFeature::Annotated(3)
PLEASE PUT SOMETHING HERE
Bio::SeqFeature::AnnotationAdaptor(3)
integrates SeqFeatureIs annotation
Bio::SeqFeature::Collection(3)
A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc
Bio::SeqFeature::CollectionI(3)
An interface for a collection of SeqFeatureI objects
Bio::SeqFeature::Computation(3)
Computation SeqFeature
Bio::SeqFeature::FeaturePair(3)
hold pair feature information e.g. blast hits
Bio::SeqFeature::Gene::Exon(3)
a feature representing an exon
Bio::SeqFeature::Gene::ExonI(3)
Interface for a feature representing an exon
Bio::SeqFeature::Gene::GeneStructure(3)
A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::GeneStructureI(3)
A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::Intron(3)
An intron feature
Bio::SeqFeature::Gene::NC_Feature(3), Bio::SeqFeature::Gene::NC_Feature.pm(3)
superclass for non-coding features
Bio::SeqFeature::Gene::Poly_A_site(3)
poly A feature
Bio::SeqFeature::Gene::Promoter(3)
Describes a promoter
Bio::SeqFeature::Gene::Transcript(3)
A feature representing a transcript
Bio::SeqFeature::Gene::TranscriptI(3)
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site
Bio::SeqFeature::Gene::UTR(3)
A feature representing an untranslated region that is part of a transcriptional unit
Bio::SeqFeature::Generic(3)
Generic SeqFeature
Bio::SeqFeature::Lite(3)
Lightweight Bio::SeqFeatureI class
Bio::SeqFeature::PositionProxy(3)
handle features when truncation/revcom sequences span a feature
Bio::SeqFeature::Primer(3)
Primer Generic SeqFeature
Bio::SeqFeature::Similarity(3)
A sequence feature based on similarity
Bio::SeqFeature::SimilarityPair(3)
Sequence feature based on the similarity of two sequences
Bio::SeqFeature::SubSeq(3)
Feature representing a subsequence
Bio::SeqFeature::Tools::FeatureNamer(3)
generates unique persistent names for features
Bio::SeqFeature::Tools::IDHandler(3)
maps $seq_feature->primary_tag
Bio::SeqFeature::Tools::TypeMapper(3)
maps $seq_feature->primary_tag
Bio::SeqFeature::Tools::Unflattener(3)
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Bio::SeqFeature::TypedSeqFeatureI(3)
a strongly typed SeqFeature
Bio::SeqFeatureI(3)
Abstract interface of a Sequence Feature
Bio::SeqI(3)
[Developers] Abstract Interface of Sequence (with features)
Bio::SeqIO(3)
Handler for SeqIO Formats
Bio::SeqIO::FTHelper(3)
Helper class for EMBL/Genbank feature tables
Bio::SeqIO::Handler::GenericRichSeqHandler(3)
Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
Bio::SeqIO::MultiFile(3)
Treating a set of files as a single input stream
Bio::SeqIO::ace(3)
ace sequence input/output stream
Bio::SeqIO::asciitree(3)
asciitree sequence input/output stream
Bio::SeqIO::bsml(3)
BSML sequence input/output stream
Bio::SeqIO::bsml_sax(3)
BSML sequence input/output stream using SAX
Bio::SeqIO::embl(3)
EMBL sequence input/output stream
Bio::SeqIO::embldriver(3)
EMBL sequence input/output stream
Bio::SeqIO::entrezgene(3)
Entrez Gene ASN1 parser
Bio::SeqIO::fasta(3)
fasta sequence input/output stream
Bio::SeqIO::fastq(3)
fastq sequence input/output stream
Bio::SeqIO::game(3)
-- a class for parsing and writing game-XML
Bio::SeqIO::game::featHandler(3)
-- a class for handling feature elements
Bio::SeqIO::game::gameHandler(3)
-- PerlSAX handler for game-XML
Bio::SeqIO::game::gameSubs(3)
-- a base class for game-XML parsing
Bio::SeqIO::game::gameWriter(3)
-- a class for writing game-XML
Bio::SeqIO::game::seqHandler(3)
-- a class for handling game-XML sequences
Bio::SeqIO::gbdriver(3)
GenBank handler-based push parser
Bio::SeqIO::gbxml(3)
GenBank sequence input/output stream using SAX
Bio::SeqIO::gcg(3)
GCG sequence input/output stream
Bio::SeqIO::genbank(3)
GenBank sequence input/output stream
Bio::SeqIO::interpro(3)
InterProScan XML input/output stream
Bio::SeqIO::kegg(3)
KEGG sequence input/output stream
Bio::SeqIO::largefasta(3)
method i/o on very large fasta sequence files
Bio::SeqIO::locuslink(3)
LocusLink input/output stream
Bio::SeqIO::mbsout(3)
input stream for output by Teshima et al.'s mbs
Bio::SeqIO::metafasta(3)
metafasta sequence input/output stream
Bio::SeqIO::msout(3)
input stream for output by Hudson's ms
Bio::SeqIO::phd(3)
phd file input/output stream
Bio::SeqIO::pir(3)
PIR sequence input/output stream
Bio::SeqIO::qual(3)
.qual file input/output stream
Bio::SeqIO::raw(3)
raw sequence file input/output stream
Bio::SeqIO::scf(3)
.scf file input/output stream
Bio::SeqIO::seqxml(3)
SeqXML sequence input/output stream
Bio::SeqIO::swiss(3)
Swissprot sequence input/output stream
Bio::SeqIO::swissdriver(3)
SwissProt/UniProt handler-based push parser
Bio::SeqIO::tab(3)
nearly raw sequence file input/output stream. Reads/writes id"et"sequence"en"
Bio::SeqIO::table(3)
sequence input/output stream from a delimited table
Bio::SeqIO::tigr(3)
TIGR XML sequence input/output stream
Bio::SeqIO::tigrxml(3)
Parse TIGR (new) XML
Bio::SeqIO::tinyseq(3)
reading/writing sequences in NCBI TinySeq format
Bio::SeqIO::tinyseq::tinyseqHandler(3)
XML event handlers to support NCBI TinySeq XML parsing
Bio::SeqUtils(3)
Additional methods for PrimarySeq objects
Bio::SimpleAlign(3)
Multiple alignments held as a set of sequences
Bio::SimpleAnalysisI(3)
A simple interface to any (local or remote) analysis tool
Bio::Species(3)
Generic species object
Bio::Taxon(3)
A node in a represented taxonomy
Bio::Tools::Alignment::Consed(3)
A module to work with objects from consed .ace files
Bio::Tools::Alignment::Trim(3)
A kludge to do specialized trimming of sequence based on quality
Bio::Tools::AmpliconSearch(3)
Find amplicons in a template using degenerate PCR primers
Bio::Tools::Analysis::SimpleAnalysisBase(3)
abstract superclass for SimpleAnalysis implementations
Bio::Tools::AnalysisResult(3)
Base class for analysis result objects and parsers
Bio::Tools::Blat(3)
parser for Blat program
Bio::Tools::CodonTable(3)
Codon table object
Bio::Tools::Coil(3)
parser for Coil output
Bio::Tools::ECnumber(3)
representation of EC numbers (Enzyme Classification)
Bio::Tools::EMBOSS::Palindrome(3)
parse EMBOSS palindrome output
Bio::Tools::EPCR(3)
Parse ePCR output and make features
Bio::Tools::ESTScan(3)
Results of one ESTScan run
Bio::Tools::Eponine(3)
Results of one Eponine run
Bio::Tools::Est2Genome(3)
Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
Bio::Tools::Fgenesh(3)
parse results of one Fgenesh run
Bio::Tools::FootPrinter(3)
write sequence features in FootPrinter format
Bio::Tools::GFF(3)
A Bio::SeqAnalysisParserI compliant GFF format parser
Bio::Tools::Geneid(3)
Results of one geneid run
Bio::Tools::Genemark(3)
Results of one Genemark run
Bio::Tools::Genewise(3)
Results of one Genewise run
Bio::Tools::Genomewise(3)
Results of one Genomewise run
Bio::Tools::Genscan(3)
Results of one Genscan run
Bio::Tools::Glimmer(3)
parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
Bio::Tools::Grail(3)
Results of one Grail run
Bio::Tools::GuessSeqFormat(3)
Module for determining the sequence format of the contents of a file, a string, or through a filehandle
Bio::Tools::IUPAC(3)
Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
Bio::Tools::Lucy(3)
Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Bio::Tools::MZEF(3)
Results of one MZEF run
Bio::Tools::Match(3)
Parses output from Transfac's match(TM)
Bio::Tools::OddCodes(3)
Object holding alternative alphabet coding for one protein sequence
Bio::Tools::Phylo::Gerp(3)
Parses output from GERP
Bio::Tools::Phylo::Molphy(3)
parser for Molphy output
Bio::Tools::Phylo::Molphy::Result(3)
container for data parsed from a ProtML run
Bio::Tools::Phylo::Phylip::ProtDist(3)
parser for ProtDist output
Bio::Tools::Prediction::Exon(3)
A predicted exon feature
Bio::Tools::Prediction::Gene(3)
a predicted gene structure feature
Bio::Tools::Primer3(3)
Create input for and work with the output from the program primer3
Bio::Tools::Primer::Assessor::Base(3)
base class for common assessor things
Bio::Tools::Primer::AssessorI(3)
interface for assessing primer pairs
Bio::Tools::Primer::Feature(3)
position of a single primer
Bio::Tools::Primer::Pair(3)
two primers on left and right side
Bio::Tools::Prints(3)
Parser for FingerPRINTScanII program
Bio::Tools::Profile(3)
parse Profile output
Bio::Tools::Promoterwise(3)
parser for Promoterwise tab format output
Bio::Tools::PrositeScan(3)
Parser for ps_scan result
Bio::Tools::Pseudowise(3)
Results of one Pseudowise run
Bio::Tools::QRNA(3)
A Parser for qrna output
Bio::Tools::RandomDistFunctions(3)
A set of routines useful for generating random data in different distributions
Bio::Tools::RepeatMasker(3)
a parser for RepeatMasker output
Bio::Tools::Run::Alignment::Amap(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program
Bio::Tools::Run::Alignment::DBA(3)
Object for the alignment of two sequences using the DNA Block Aligner program
Bio::Tools::Run::Alignment::Gmap(3)
Wrapper for running gmap
Bio::Tools::Run::Alignment::Kalign(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program
Bio::Tools::Run::Alignment::Lagan(3)
Object for the local execution of the LAGAN suite of tools (including MLAGAN for multiple sequence alignments)
Bio::Tools::Run::Alignment::MAFFT(3)
run the MAFFT alignment tools
Bio::Tools::Run::Alignment::MSAProbs(3)
Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program
Bio::Tools::Run::Alignment::Muscle(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program
Bio::Tools::Run::Alignment::Pal2Nal(3)
Wrapper for Pal2Nal
Bio::Tools::Run::Alignment::Probalign(3)
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program
Bio::Tools::Run::Alignment::Probcons(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program
Bio::Tools::Run::Alignment::Proda(3)
Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program
Bio::Tools::Run::Alignment::Sim4(3)
Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
Bio::Tools::Run::Alignment::StandAloneFasta(3)
Object for the local execution of the Fasta3 programs ((t)fasta3, (t)fastx3, (t)fasty3 ssearch3)
Bio::Tools::Run::Analysis(3)
Module representing any (remote or local) analysis tool
Bio::Tools::Run::Analysis::soap(3)
A SOAP-based access to the analysis tools
Bio::Tools::Run::AnalysisFactory(3)
A directory of analysis tools
Bio::Tools::Run::AnalysisFactory::soap(3)
A SOAP-based access to the list of analysis tools
Bio::Tools::Run::BEDTools(3)
Run wrapper for the BEDTools suite of programs *BETA*
Bio::Tools::Run::BEDTools::Config(3)
Configuration data for bowtie commands
Bio::Tools::Run::BlastPlus(3)
A wrapper for NCBI's blast+ suite
Bio::Tools::Run::Coil(3)
wrapper for ncoils program
Bio::Tools::Run::EMBOSSApplication(3)
class for EMBOSS Applications
Bio::Tools::Run::EMBOSSacd(3)
class for EMBOSS Application qualifiers
Bio::Tools::Run::ERPIN(3)
Wrapper for local execution of the ERPIN suite of programs
Bio::Tools::Run::Ensembl(3)
A simplified front-end for setting up the registry for, and then using an Ensembl database with the Ensembl Perl API
Bio::Tools::Run::Eponine(3)
Object for execution of the Eponine which is a mammalian TSS predictor
Bio::Tools::Run::FootPrinter(3)
wrapper for the FootPrinter program
Bio::Tools::Run::Genemark(3)
Wrapper for local execution of the GeneMark family of programs
Bio::Tools::Run::GenericParameters(3)
An object for the parameters used to run programs
Bio::Tools::Run::Genewise(3)
Object for predicting genes in a given sequence given a protein
Bio::Tools::Run::Genscan(3)
Object for identifying genes in a given sequence given a matrix(for appropriate organisms)
Bio::Tools::Run::Glimmer(3)
Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM
Bio::Tools::Run::Hmmer(3)
Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
Bio::Tools::Run::Infernal(3)
Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore
Bio::Tools::Run::MCS(3)
Wrapper for MCS
Bio::Tools::Run::Match(3)
Wrapper for Transfac's match(TM)
Bio::Tools::Run::Mdust(3), Mdust(3)
Perl extension for Mdust nucleotide filtering
Bio::Tools::Run::ParametersI(3)
A Base object for the parameters used to run programs
Bio::Tools::Run::Phylo::Gerp(3), Bio::Tools::Run::Gerp(3)
Wrapper for GERP
Bio::Tools::Run::Phylo::Hyphy::Base(3)
Hyphy wrapping base methods
Bio::Tools::Run::Phylo::Hyphy::BatchFile(3)
Wrapper for custom execution of Hyphy batch files
Bio::Tools::Run::Phylo::Hyphy::FEL(3)
Wrapper around the Hyphy FEL analysis
Bio::Tools::Run::Phylo::Hyphy::Modeltest(3)
Wrapper around the Hyphy Modeltest analysis
Bio::Tools::Run::Phylo::Hyphy::REL(3)
Wrapper around the Hyphy REL analysis
Bio::Tools::Run::Phylo::Hyphy::SLAC(3)
Wrapper around the Hyphy SLAC analysis
Bio::Tools::Run::Phylo::LVB(3)
Object for using the LVB program to create an array of Bio::Tree objects from a nucleotide multiple alignment file or a nucleotide SimpleAlign object. Works with LVB version 2.1
Bio::Tools::Run::Phylo::Molphy::ProtML(3)
A wrapper for the Molphy pkg app ProtML
Bio::Tools::Run::Phylo::Njtree::Best(3)
Wrapper around the Njtree (Njtree/phyml) best program
Bio::Tools::Run::Phylo::Phast::PhastCons(3)
Wrapper for footprinting using phastCons
Bio::Tools::Run::Phylo::Phast::PhyloFit(3)
Wrapper for phyloFit
Bio::Tools::Run::Phylo::Phylip::Base(3)
Base object for Phylip modules
Bio::Tools::Run::Phylo::Phylip::Consense(3)
Wrapper for the phylip program Consense
Bio::Tools::Run::Phylo::Phylip::DrawGram(3)
use Phylip DrawTree program to draw phylograms or phenograms
Bio::Tools::Run::Phylo::Phylip::DrawTree(3)
use Phylip DrawTree program to draw trees
Bio::Tools::Run::Phylo::Phylip::Neighbor(3)
Wrapper for the phylip program neighbor by Joseph Felsenstein for creating a phylogenetic tree(either through Neighbor or UPGMA) based on protein distances based on amino substitution rate. 14 Nov 2002 Shawn Works with Phylip version 3.6
Bio::Tools::Run::Phylo::Phylip::ProtDist(3)
Wrapper for the phylip program protdist
Bio::Tools::Run::Phylo::Phylip::ProtPars(3)
Object for creating a Bio::Tree object from a multiple alignment file or a SimpleAlign object 14 Nov 2002 Shawn Works with Phylip version 3.6
Bio::Tools::Run::Phylo::Phylip::SeqBoot(3)
Wrapper for the phylip program SeqBoot
Bio::Tools::Run::Phylo::PhyloBase(3), Bio::Tools::Run::Phylo::PhyloBase-(3)
base module for phylo wrappers
Bio::Tools::Run::Phylo::Phyml(3)
Wrapper for rapid reconstruction of phylogenies using Phyml
Bio::Tools::Run::Phylo::QuickTree(3)
Wrapper for rapid reconstruction of phylogenies using QuickTree
Bio::Tools::Run::Phylo::SLR(3)
Wrapper around the SLR program
Bio::Tools::Run::Phylo::Semphy(3)
Wrapper for Semphy
Bio::Tools::Run::Primate(3), Wrapper(3)
for Primate, Guy Slater's near exact match finder for short sequence tags
Bio::Tools::Run::Primer3(3)
Create input for and work with the output from the program primer3
Bio::Tools::Run::Promoterwise(3)
Wrapper for aligning two sequences using promoterwise
Bio::Tools::Run::Pseudowise(3)
Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence
Bio::Tools::Run::RNAMotif(3)
Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune
Bio::Tools::Run::RepeatMasker(3)
Wrapper for RepeatMasker Program
Bio::Tools::Run::Samtools(3)
a run wrapper for the samtools suite *BETA*
Bio::Tools::Run::Samtools::Config(3)
configurator for Bio::Tools::Run::Samtools
Bio::Tools::Run::Seg(3)
Object for identifying low complexity regions in a given protein seequence
Bio::Tools::Run::Simprot(3)
Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
Bio::Tools::Run::StandAloneBlast(3)
Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast
Bio::Tools::Run::StandAloneBlastPlus(3)
Compute with NCBI's blast+ suite *ALPHA*
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3)
Provides BLAST methods to StandAloneBlastPlus
Bio::Tools::Run::StandAloneNCBIBlast(3)
Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast
Bio::Tools::Run::StandAloneWUBlast(3)
Object for the local execution of WU-Blast
Bio::Tools::Run::Tmhmm(3)
Object for identifying transmembrane helixes in a given protein seequence
Bio::Tools::Run::Vista(3)
Wrapper for Vista
Bio::Tools::Run::WrapperBase(3)
A Base object for wrappers around executables
Bio::Tools::Run::WrapperBase::CommandExts(3)
Extensions to WrapperBase for handling programs with commands *ALPHA*
Bio::Tools::Run::tRNAscanSE(3)
Wrapper for local execution of tRNAscan-SE
Bio::Tools::Seg(3)
parse "seg" output
Bio::Tools::SeqPattern(3)
represent a sequence pattern or motif
Bio::Tools::SeqPattern::Backtranslate(3)
reverse translate protein patterns
Bio::Tools::SeqStats(3)
Object holding statistics for one particular sequence
Bio::Tools::SeqWords(3)
Object holding n-mer statistics for a sequence
Bio::Tools::Sigcleave(3)
Bioperl object for sigcleave analysis
Bio::Tools::Signalp(3)
parser for Signalp output
Bio::Tools::Signalp::ExtendedSignalp(3)
enhanced parser for Signalp output
Bio::Tools::Sim4::Exon(3)
A single exon determined by an alignment
Bio::Tools::Sim4::Results(3)
Results of one Sim4 run
Bio::Tools::Spidey::Exon(3)
A single exon determined by an alignment
Bio::Tools::Spidey::Results(3)
Results of a Spidey run
Bio::Tools::TandemRepeatsFinder(3)
a parser for Tandem Repeats Finder output
Bio::Tools::TargetP(3)
Results of one TargetP run
Bio::Tools::Tmhmm(3)
parse TMHMM output (TransMembrane HMM)
Bio::Tools::ipcress(3)
Parse ipcress output and make features
Bio::Tools::isPcr(3)
Parse isPcr output and make features
Bio::Tools::pICalculator(3)
calculate the isoelectric point of a protein
Bio::Tools::tRNAscanSE(3)
A parser for tRNAscan-SE output
Bio::Tree::AnnotatableNode(3)
A Tree Node with support for annotation
Bio::Tree::Compatible(3)
Testing compatibility of phylogenetic trees with nested taxa
Bio::Tree::DistanceFactory(3)
Construct a tree using distance based methods
Bio::Tree::Node(3)
A Simple Tree Node
Bio::Tree::NodeI(3)
Interface describing a Tree Node
Bio::Tree::NodeNHX(3)
A Simple Tree Node with support for NHX tags
Bio::Tree::RandomFactory(3)
TreeFactory for generating Random Trees
Bio::Tree::Statistics(3)
Calculate certain statistics for a Tree
Bio::Tree::Tree(3)
An implementation of the TreeI interface
Bio::Tree::TreeFunctionsI(3)
Decorated Interface implementing basic Tree exploration methods
Bio::Tree::TreeI(3)
A Tree object suitable for lots of things, designed originally for Phylogenetic Trees
Bio::TreeIO(3)
Parser for Tree files
Bio::TreeIO::NewickParser(3)
newick string parser
Bio::TreeIO::TreeEventBuilder(3)
Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
Bio::TreeIO::cluster(3)
A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
Bio::TreeIO::lintree(3)
Parser for lintree output trees
Bio::TreeIO::newick(3)
parsing and writing of Newick/PHYLIP/New Hampshire format
Bio::TreeIO::nexus(3)
A TreeIO driver module for parsing Nexus tree output from PAUP
Bio::TreeIO::nhx(3)
TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format
Bio::TreeIO::pag(3)
Bio::TreeIO driver for Pagel format
Bio::TreeIO::phyloxml(3)
TreeIO implementation for parsing PhyloXML format
Bio::TreeIO::tabtree(3)
A simple output format which displays a tree as an ASCII drawing
Bio::UpdateableSeqI(3)
Descendant of Bio::SeqI that allows updates
Bio::Variation::AAChange(3)
Sequence change class for polypeptides
Bio::Variation::AAReverseMutate(3)
point mutation and codon information from single amino acid changes
Bio::Variation::Allele(3)
Sequence object with allele-specific attributes
Bio::Variation::DNAMutation(3)
DNA level mutation class
Bio::Variation::IO(3)
Handler for sequence variation IO Formats
Bio::Variation::IO::flat(3)
flat file sequence variation input/output stream
Bio::Variation::IO::xml(3)
XML sequence variation input/output stream
Bio::Variation::RNAChange(3)
Sequence change class for RNA level
Bio::Variation::SNP(3)
submitted SNP
Bio::Variation::SeqDiff(3)
Container class for mutation/variant descriptions
Bio::Variation::VariantI(3)
Sequence Change SeqFeature abstract class
Bio::WebAgent(3)
A base class for Web (any protocol) access
BioPerl(3)
Perl modules for biology
Color::Library::Dictionary::NBS_ISCC::B(3)
(NBS/ISCC B) Colour Terminology in Biology
Net::NBName(3)
NetBIOS Name Service Requests
Net::NBName::NameQuery(3)
NetBIOS Name Query Response
Net::NBName::NameQuery::RR(3)
NetBIOS Name Query Response Resource Record
Net::NBName::NodeStatus(3)
NetBIOS Node Status Response
Net::NBName::NodeStatus::RR(3)
NetBIOS Node Status Response Resource Record
Ocsinventory::Agent::Common(3)
give common methods to other modules "addController()" 4 Item "addController()" Add a controller in the inventory. "addUsb()" 4 Item "addUsb()" Add external usb devices in the inventory. "addInput()" 4 Item "addInput()" Add internal inputs as keyboard, mouse in the inventory. "addModem()" 4 Item "addModem()" Add a modem in the inventory. "addDrive()" 4 Item "addDrive()" Add a partition in the inventory. "addStorages()" 4 Item "addStorages()" Add a storage system (hard drive, USB key, SAN volume, etc) in the inventory. "addMemory()" 4 Item "addMemory()" Add a memory module in the inventory. "addPort()" 4 Item "addPort()" Add a port module in the inventory. "addSlot()" 4 Item "addSlot()" Add a slot in the inventory. "addSoftware()" 4 Item "addSoftware()" Register a software in the inventory. "addMonitor()" 4 Item "addMonitor()" Add a monitor (screen) in the inventory. "addVideo()" 4 Item "addVideo()" Add a video card in the inventory. "addSound()" 4 Item "addSound()" Add a sound card in the inventory. "addNetwork()" 4 Item "addNetwork()" Register a network in the inventory. "addRepo()" 4 Item "addRepo()" Register a repository in the inventory. "setHardware()" 4 Item "setHardware()" Save global information regarding the machine. The use of setHardware() to update USERID and PROCESSOR* information is deprecated, please, use addUser() and addCPU() instead. "setBios()" 4 Item "setBios()" Set BIOS information. "addCPU()" 4 Item "addCPU()" Add a CPU in the inventory. "addUser()" 4 Item "addUser()" Add an user in the list of logged user. "addLocalUser()" 4 Item "addLocalUser()" Add local users in the inventory. "addLocalGroup()" 4 Item "addLocalGroup()" Add local groups in the inventory. "addPrinter()" 4 Item "addPrinter()" Add a printer in the inventory. "addVirtualMachine()" 4 Item "addVirtualMachine()" Add a Virtual Machine in the inventory. "addProcess()" 4 Item "addProcess()" Record a running process in the inventory. "addCamera()" 4 Item "addCamera()" Add a camera device in the inventory. Only avalaible for MacOSX "addIpDiscoverEntry()" 4 Item "addIpDiscoverEntry()" IpDiscover is used to identify network interface on the local network. This is done on the ARP level. This function adds a network interface in the inventory. "setAccessLog()" 4 Item "setAccessLog()" What is that for? :) "flushXMLTags()" 4 Item "flushXMLTags()" Clear the content of $common->{xmltags} (to use after adding it in XML) "addBatteries()" 4 Item "addBatteries()" Add a memory module in the inventory
Win32::DBIODBC(3)
Win32::ODBC emulation layer for the DBI
bio(3), Bopen(3), Bfdopen(3), Binit(3), Binits(3), Brdline(3), Brdstr(3), Bgetc(3), Bgetrune(3), Bgetd(3), Bungetc(3), Bungetrune(3), Bread(3), Bseek(3), Boffset(3), Bfildes(3), Blinelen(3), Bputc(3), Bputrune(3), Bprint(3), Bvprint(3), Bwrite(3), Bflush(3), Bterm(3), Bbuffered(3)
buffered input/output
biosdecode(8)
BIOS information decoder
bp_biofetch_genbank_proxy(1), bp_biofetch_genbank_proxy.pl(1)
Caching BioFetch-compatible web proxy for GenBank
bp_bioflat_index(1), bp_bioflat_index.pl(1)
index sequence files using Bio::DB::Flat
bp_biogetseq(1)
sequence retrieval using OBDA registry
bp_fetch(1), bp_fetch.pl(1)
fetches sequences from bioperl indexed databases
bp_seqconvert(1)
generic BioPerl sequence format converter
bp_seqret(1)
bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
bp_tree2pag(1)
convert Bio::TreeIO parseable format trees to pagel format
feature_draw.pl(1)
-- Render a Bio::Graphics Feature File
frend.pl(1)
-- Render a Bio::Graphics Feature File on the web
i.biomass(1), i.biomass (1)
Computes biomass growth, precursor of crop yield calculation
home | help