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Mat_VarGetStructFieldnames(3)
Get the fieldnames of a structure variable
SDL_CDName(3)
Returns a human-readable, system-dependent identifier for the CD-ROM
TIFFFieldName(3tiff)
Get TIFF field name from field information
Tcl_AppendExportList.tcl85(3), Tcl_AppendExportList(3), Tcl_CreateNamespace(3), Tcl_DeleteNamespace(3), Tcl_Export(3), Tcl_FindCommand(3), Tcl_FindNamespace(3), Tcl_ForgetImport(3), Tcl_GetCurrentNamespace(3), Tcl_GetGlobalNamespace(3), Tcl_GetNamespaceUnknownHandler(3), Tcl_Import(3), Tcl_SetNamespaceUnknownHandler(3)
manipulate namespaces
Tcl_AppendExportList.tcl86(3), Tcl_AppendExportList(3), Tcl_CreateNamespace(3), Tcl_DeleteNamespace(3), Tcl_Export(3), Tcl_FindCommand(3), Tcl_FindNamespace(3), Tcl_ForgetImport(3), Tcl_GetCurrentNamespace(3), Tcl_GetGlobalNamespace(3), Tcl_GetNamespaceUnknownHandler(3), Tcl_Import(3), Tcl_SetNamespaceUnknownHandler(3)
manipulate namespaces
Tcl_AppendExportList.tcl87(3), Tcl_AppendExportList(3), Tcl_CreateNamespace(3), Tcl_DeleteNamespace(3), Tcl_Export(3), Tcl_FindCommand(3), Tcl_FindNamespace(3), Tcl_ForgetImport(3), Tcl_GetCurrentNamespace(3), Tcl_GetGlobalNamespace(3), Tcl_GetNamespaceUnknownHandler(3), Tcl_Import(3), Tcl_SetNamespaceUnknownHandler(3)
manipulate namespaces
Tcl_ClassGetMetadata.tcl86(3), Tcl_ClassGetMetadata(3), Tcl_ClassSetMetadata(3), Tcl_CopyObjectInstance(3), Tcl_GetClassAsObject(3), Tcl_GetObjectAsClass(3), Tcl_GetObjectCommand(3), Tcl_GetObjectFromObj(3), Tcl_GetObjectName(3), Tcl_GetObjectNamespace(3), Tcl_NewObjectInstance(3), Tcl_ObjectDeleted(3), Tcl_ObjectGetMetadata(3), Tcl_ObjectGetMethodNameMapper(3), Tcl_ObjectSetMetadata(3), Tcl_ObjectSetMethodNameMapper(3)
manipulate objects and classes
Tcl_ClassGetMetadata.tcl87(3), Tcl_ClassGetMetadata(3), Tcl_ClassSetMetadata(3), Tcl_CopyObjectInstance(3), Tcl_GetClassAsObject(3), Tcl_GetObjectAsClass(3), Tcl_GetObjectCommand(3), Tcl_GetObjectFromObj(3), Tcl_GetObjectName(3), Tcl_GetObjectNamespace(3), Tcl_NewObjectInstance(3), Tcl_ObjectDeleted(3), Tcl_ObjectGetMetadata(3), Tcl_ObjectGetMethodNameMapper(3), Tcl_ObjectSetMetadata(3), Tcl_ObjectSetMethodNameMapper(3)
manipulate objects and classes
Tcl_ClassSetConstructor.tcl86(3), Tcl_ClassSetConstructor(3), Tcl_ClassSetDestructor(3), Tcl_MethodDeclarerClass(3), Tcl_MethodDeclarerObject(3), Tcl_MethodIsPublic(3), Tcl_MethodIsType(3), Tcl_MethodName(3), Tcl_NewInstanceMethod(3), Tcl_NewMethod(3), Tcl_ObjectContextInvokeNext(3), Tcl_ObjectContextIsFiltering(3), Tcl_ObjectContextMethod(3), Tcl_ObjectContextObject(3), Tcl_ObjectContextSkippedArgs(3)
manipulate methods and method-call contexts
Tcl_ClassSetConstructor.tcl87(3), Tcl_ClassSetConstructor(3), Tcl_ClassSetDestructor(3), Tcl_MethodDeclarerClass(3), Tcl_MethodDeclarerObject(3), Tcl_MethodIsPublic(3), Tcl_MethodIsPrivate(3), Tcl_MethodIsType(3), Tcl_MethodName(3), Tcl_NewInstanceMethod(3), Tcl_NewMethod(3), Tcl_ObjectContextInvokeNext(3), Tcl_ObjectContextIsFiltering(3), Tcl_ObjectContextMethod(3), Tcl_ObjectContextObject(3), Tcl_ObjectContextSkippedArgs(3)
manipulate methods and method-call contexts
Tcl_CreateObjCommand.tcl85(3), Tcl_CreateObjCommand(3), Tcl_DeleteCommand(3), Tcl_DeleteCommandFromToken(3), Tcl_GetCommandInfo(3), Tcl_GetCommandInfoFromToken(3), Tcl_SetCommandInfo(3), Tcl_SetCommandInfoFromToken(3), Tcl_GetCommandName(3), Tcl_GetCommandFullName(3), Tcl_GetCommandFromObj(3)
implement new commands in C
Tcl_CreateObjCommand.tcl86(3), Tcl_CreateObjCommand(3), Tcl_DeleteCommand(3), Tcl_DeleteCommandFromToken(3), Tcl_GetCommandInfo(3), Tcl_GetCommandInfoFromToken(3), Tcl_SetCommandInfo(3), Tcl_SetCommandInfoFromToken(3), Tcl_GetCommandName(3), Tcl_GetCommandFullName(3), Tcl_GetCommandFromObj(3)
implement new commands in C
Tcl_CreateObjCommand.tcl87(3), Tcl_CreateObjCommand(3), Tcl_DeleteCommand(3), Tcl_DeleteCommandFromToken(3), Tcl_GetCommandInfo(3), Tcl_GetCommandInfoFromToken(3), Tcl_SetCommandInfo(3), Tcl_SetCommandInfoFromToken(3), Tcl_GetCommandName(3), Tcl_GetCommandFullName(3), Tcl_GetCommandFromObj(3), Tcl_RegisterCommandTypeName(3), Tcl_GetCommandTypeName(3)
implement new commands in C
Tcl_ZlibAdler32.tcl86(3), Tcl_ZlibAdler32(3), Tcl_ZlibCRC32(3), Tcl_ZlibDeflate(3), Tcl_ZlibInflate(3), Tcl_ZlibStreamChecksum(3), Tcl_ZlibStreamClose(3), Tcl_ZlibStreamEof(3), Tcl_ZlibStreamGet(3), Tcl_ZlibStreamGetCommandName(3), Tcl_ZlibStreamInit(3), Tcl_ZlibStreamPut(3)
compression and decompression functions
Tcl_ZlibAdler32.tcl87(3), Tcl_ZlibAdler32(3), Tcl_ZlibCRC32(3), Tcl_ZlibDeflate(3), Tcl_ZlibInflate(3), Tcl_ZlibStreamChecksum(3), Tcl_ZlibStreamClose(3), Tcl_ZlibStreamEof(3), Tcl_ZlibStreamGet(3), Tcl_ZlibStreamGetCommandName(3), Tcl_ZlibStreamInit(3), Tcl_ZlibStreamPut(3)
compression and decompression functions
align(1)
compute the global alignment of two protein or DNA sequences align0 - compute the global alignment of two protein or DNA sequences without penalizing for end-gaps
ceph-rbdnamer(8)
udev helper to name RBD devices rst2man-indent-level 0 1 rstReportMargin \$1
fasta(1)
scan a protein or DNA sequence library for similar sequences tfasta - compare a protein sequence to a DNA sequence library, translating the DNA sequence library `on-the-fly'. lfasta - compare two protein or DNA sequences for local similarity and show the local sequence alignments plfasta - compare two sequences for local similarity and plot the local sequence alignments
fasta36(1)
scan a protein or DNA sequence library for similar sequences fastx36 - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames. tfastx36 - compare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations. fasty36 - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames. tfasty36 - compare a protein sequence to a DNA sequence database, calculating similarities with frameshifts to the forward and reverse orientations. fasts36 - compare unordered peptides to a protein sequence database fastm36 - compare ordered peptides (or short DNA sequences) to a protein (DNA) sequence database tfasts36 - compare unordered peptides to a translated DNA sequence database fastf36 - compare mixed peptides to a protein sequence database tfastf36 - compare mixed peptides to a translated DNA sequence database ssearch36 - compare a protein or DNA sequence to a sequence database using the Smith-Waterman algorithm. ggsearch36 - compare a protein or DNA sequence to a sequence database using a global alignment (Needleman-Wunsch) glsearch36 - compare a protein or DNA sequence to a sequence database with alignments that are global in the query and local in the database sequence (global-local). lalign36 - produce multiple non-overlapping alignments for protein and DNA sequences using the Huang and Miller sim algorithm for the Waterman-Eggert algorithm. prss36, prfx36 - discontinued; all the FASTA programs will estimate statistical significance using 500 shuffled sequence scores if two sequences are compared
fastf3(1), fastf3_t(1)
compare a mixed peptide sequence against a protein database using a modified fasta algorithm. tfastf3, tfastf3_t - compare a mixed pepide sequence against a translated DNA database
fasts3(1), fasts3_t(1)
compare several short peptide sequences against a protein database using a modified fasta algorithm. tfasts3, tfasts3_t - compare short pepides against a translated DNA database
getdns_convert(3)
getdns_convert_dns_name_to_fqdn, getdns_convert_fqdn_to_dns_name -- convert dname between presentation- and wire-format
glLoadName(3), "glLoadName(3)
load a name onto the name stack
gnutls_idna_map(3)
API function
gnutls_idna_reverse_map(3)
API function
idn.conf(5), .idnrc(5), idnalias.conf(5)
configuration files for idnkit library
idn_version_unicode(3), idn_version_idnatable(3), idn_version_libidn(3), idn_version_getstring(3)
get a version string about idnkit
idna_strerror(3)
API function
idna_to_ascii_4i(3)
API function
idna_to_ascii_4z(3)
API function
idna_to_ascii_8z(3)
API function
idna_to_ascii_lz(3)
API function
idna_to_unicode_44i(3)
API function
idna_to_unicode_4z4z(3)
API function
idna_to_unicode_8z4z(3)
API function
idna_to_unicode_8z8z(3)
API function
idna_to_unicode_8zlz(3)
API function
idna_to_unicode_lzlz(3)
API function
idnalias.conf(5)
encoding alias file for idnkit
jellyfish(1), Jellyfish(1)
is a software to count k-mers in DNA sequences
lalign(1)
compare two protein or DNA sequences for local similarity and show the local sequence alignments plalign,flalign - compare two sequences for local similarity and plot the local sequence alignments
ldns_dname2canonical(3)
canonicalize dname
ldns_dname_cat_clone(3), ldns_dname_cat(3)
concatenate two dnames
ldns_dname_compare(3), ldns_dname_interval(3)
compare two dnames
ldns_dname_is_subdomain(3), ldns_dname_str_absolute(3), ldns_dname_label(3)
check properties of dnames
ldns_dname_left_chop(3), ldns_dname_label_count(3)
dname label functions
ldns_dname_new(3), ldns_dname_new_frm_str(3), ldns_dname_new_frm_data(3)
create a dname
ldns_rr_ns_nsdname(3)
get dname rdata field from NS RR
ldns_wire2rr(3), ldns_wire2pkt(3), ldns_wire2rdf(3), ldns_wire2dname(3)
convert from wire format to host type
minimap2(1)
mapping and alignment between collections of DNA sequences
ne_ssl_readable_dname(3), ne_ssl_dname_cmp(3)
SSL distinguished name handling
nhmmer(1)
search DNA queries against a DNA sequence database
nhmmscan(1)
search DNA sequence(s) against a DNA profile database
randseq(1)
randomly shuffle a protein or DNA sequence
ssearch(1)
scan a protein or DNA sequence library for similar sequences
tcl_idna.tcl87(n), tcl::idna(n)
Support for normalization of Internationalized Domain Names
Bio::Align::DNAStatistics(3)
Calculate some statistics for a DNA alignment
Bio::Das::Request::Dnas(3)
The DAS "dna" request
Bio::Graphics::Glyph::dna(3)
The "dna" glyph
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::Phylo::Matrices::Datatype::Dna(3)
Validator subclass, no serviceable parts inside
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::Seq::EncodedSeq(3)
subtype of Bio::LocatableSeq to store DNA that encodes a protein
Bio::Tools::Run::Alignment::DBA(3)
Object for the alignment of two sequences using the DNA Block Aligner program
Bio::Tools::Run::Alignment::Sim4(3)
Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
Bio::Tools::Run::Pseudowise(3)
Object for prediting pseudogenes in a given sequence given a protein and a cdna sequence
Bio::Variation::DNAMutation(3)
DNA level mutation class
DNS::LDNS::DNSSecName(3)
Dname with rrsets in a dnssec zone
DNS::LDNS::RData(3)
Rdata field or a dname in an rr
Net::DNS::RR::DNAME(3)
DNS DNAME resource record
Net::IDN::Encode(3)
Internationalizing Domain Names in Applications (IDNA)
Net::IDN::Overview(3), Net::IDN::Overwiew(3)
Internationalized Domain Names for Applications (IDNA)
Net::IDN::Punycode(3)
A Bootstring encoding of Unicode for IDNA (RFC 3492)
Net::IDN::Standards(3)
-- Internationalized Domain Names for Applications (IDNA)
Net::IDN::UTS46(3)
Unicode IDNA Compatibility Processing (UTS #46)
Perl::Critic::Policy::Bangs::ProhibitNumberedNames(3)
Prohibit variables differentiated by trailing numbers
Perl::Critic::Policy::Documentation::RequirePackageMatchesPodName(3)
The "=head1 NAME" section should match the package
Perl::Critic::Policy::Variables::ProhibitReusedNames(3)
Do not reuse a variable name in a lexical scope
bp_find-blast-matches(1), bp_find-blast-matches.pl(1)
extract DNA sequences based on BLAST hits
bp_make_mrna_protein(1)
Convert an input mRNA/cDNA sequence into protein
bp_mutate(1), bp_mutate.pl(1)
randomly mutagenize a single protein or DNA sequence
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