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FreeBSD Ports: Biology

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Software related to biology.

FastTree-2.1.8_3
Approximately-maximum-likelihood phylogenetic trees from alignments
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

InsightToolkit-4.12.2
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@FreeBSD.org
Requires: binutils-2.28,1, ca_root_nss-3.32.1, cmake-3.9.4, curl-7.56.0, expat-2.2.1, fftw-2.1.5_15, gcc-ecj-4.5, gcc6-6.4.0_2, gdcm-2.6.3_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, jsoncpp-1.8.1_2, lcms2-2.8, libarchive-3.3.1,1, libffi-3.2.1_1, liblz4-1.8.0,1, libnghttp2-1.26.0, libuv-1.15.0, lzo2-2.10_1, mpc-1.0.3, mpfr-3.1.6, ninja-1.8.2,2, openjpeg15-1.5.2_1, png-1.6.34, python27-2.7.14_1, readline-7.0.3, rhash-1.3.4, tiff-4.0.8
Also listed in: Science

afni-2015.11.13_5
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: R-3.4.2, avahi-app-0.6.31_5, binutils-2.28,1, ca_root_nss-3.32.1, cairo-1.14.8_1,2, cups-2.2.3, curl-7.56.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, dri3proto-1.0, encodings-1.0.4_3,1, endian-1.1, expat-2.2.1, f2c-20060810_5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gcc-ecj-4.5, gcc6-6.4.0_2, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, gettext-tools-0.19.8.1, ghostscript9-agpl-base-9.16_5, glib-2.50.2_6,1, glproto-1.4.17, gmake-4.2.1_1, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, graphite2-1.3.10, gsfonts-8.11_8, gsl-2.4, harfbuzz-1.5.1_1, hdf-szip-2.1_2, hdf5-1.10.1_1, icu-59.1,1, indexinfo-0.2.6, inputproto-2.3.2, jasper-1.900.1_17, jbig2dec-0.14, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, lcms2-2.8, libGLU-9.0.0_3, libGLw-8.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.83,1, libffi-3.2.1_1, libfontenc-1.1.3_1, libiconv-1.14_11, libidn-1.33_1, libidn2-2.0.4, libnghttp2-1.26.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.12, libunistring-0.9.7, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, m4-1.4.18,1, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpeg_encode-1.5b, mpfr-3.1.6, netcdf-4.5.0, netcdf-fortran-4.4.4_4, netpbm-10.80.00, nettle-3.3, open-motif-2.3.7, p11-kit-0.23.9, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python2-2_3, python27-2.7.14_1, qhull5-1.0_3, readline-7.0.3, renderproto-0.11.1, scrnsaverproto-1.2.2, svgalib-1.4.3_7, tcl86-8.6.7, tiff-4.0.8, tk86-8.6.7, tpm-emulator-0.7.4_2, trousers-0.3.14_1, wget-1.19.1_1, xbitmaps-1.1.1, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Science, Graphics

ariadne-1.3
Programs to compare protein sequences and profiles
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6

artemis-9_2
DNA sequence viewer and annotation tool
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.1.2, dejavu-2.37, expat-2.2.1, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.8, giflib-5.1.4, inputproto-2.3.2, java-zoneinfo-2017.b, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.144.1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
Also listed in: Java

avida-2.12.4
Auto-adaptive genetic system designed for ALife research
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.32.1, cmake-3.9.4, curl-7.56.0, expat-2.2.1, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, jsoncpp-1.8.1_2, libarchive-3.3.1,1, libffi-3.2.1_1, liblz4-1.8.0,1, libnghttp2-1.26.0, libuv-1.15.0, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.14_1, readline-7.0.3, rhash-1.3.4

babel-1.6_4
Converts among various molecular file formats
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Also listed in: Converters

bcftools-1.3.1_2
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: ca_root_nss-3.32.1, curl-7.56.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gsl-2.4, htslib-1.3.1, indexinfo-0.2.6, libnghttp2-1.26.0

bedtools-2.25.0
Toolset for genome arithmetic
Long description | Changes | Main Web Site
Maintained by: scottcheloha@gmail.com
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libffi-3.2.1_1, python27-2.7.14_1, readline-7.0.3

biococoa-2.2.2_3
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: theraven@FreeBSD.org
Requires: avahi-app-0.6.31_5, ca_root_nss-3.32.1, cairo-1.14.8_1,2, cups-2.2.3, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dri2proto-2.8, expat-2.2.1, fixesproto-5.0, flac-1.3.2, flite-1.4_1, fontconfig-2.12.1,1, freetype2-2.8, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, gmake-4.2.1_1, gmp-6.1.2, gnome_subr-1.0, gnustep-back-0.25.1, gnustep-base-1.25.0_1, gnustep-gui-0.25.1_1, gnustep-make-2.7.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, icu-59.1,1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcursor-1.1.14_4, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libao-1.2.0_3, libdaemon-0.14_1, libdrm-2.4.83,1, libffi-3.2.1_1, libgcrypt-1.8.1, libgpg-error-1.27, libiconv-1.14_11, libidn2-2.0.4, libobjc2-1.8.1, libogg-1.3.2_2,4, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libsndfile-1.0.28, libtasn1-4.12, libunistring-0.9.7, libunwind-20170113_1, libvorbis-1.3.5_1,3, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, libxslt-1.1.29_1, mesa-libs-17.2.2, nettle-3.3, p11-kit-0.23.9, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, png-1.6.34, python2-2_3, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, tpm-emulator-0.7.4_2, trousers-0.3.14_1, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.31
Also listed in: Gnustep

blat-36
Fast tool for local sequence similarity searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libedit-3.1.20170329_2,1, libevent-2.1.8, liblz4-1.8.0,1, mysql56-client-5.6.38, perl5-5.24.3, png-1.6.34

bowtie-1.1.2_4
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, perl5-5.24.3, python27-2.7.14_1, readline-7.0.3

bowtie2-2.3.0_2
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libffi-3.2.1_1, perl5-5.24.3, python27-2.7.14_1, readline-7.0.3, tbb-2018

bwa-0.7.9a
Burrows-Wheeler sequence aligner
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: perl5-5.24.3

cd-hit-4.6.6_2
Clustering and comparing protein or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

cdbfasta-2010.07.22
Fast indexing and retrieval of FASTA records from flat file databases
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6

chemeq-1.50_2
Outputs LaTeX code for chemical reaction
Long description | Changes
Maintained by: ports@FreeBSD.org
Requires: bison-3.0.4,1, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, m4-1.4.18,1
Also listed in: Textproc

clustalw-2.1_1
Multiple alignment program for DNA or proteins
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

consed-27.0
Graphical tool for editing Phrap assemblies
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: linux-c6-expat-2.0.1_5, linux-c6-fontconfig-2.8.0_3, linux-c6-xorg-libs-7.4_10, linux_base-c6-6.9_3, perl5-5.24.3, phrap-1.090518, phred-0.020425.c

crux-1.2.0_8
Software toolkit for phylogenetic inference
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, python27-2.7.14_1, readline-7.0.3
Also listed in: Python

cycle-0.3.1_10
Calendar program for women
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_2, atk-2.24.0, avahi-app-0.6.31_5, ca_root_nss-3.32.1, cairo-1.14.8_1,2, cantarell-fonts-0.0.25, compositeproto-0.4.2, cups-2.2.3, curl-7.56.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dconf-0.26.1, dejavu-2.37, dri2proto-2.8, enchant-1.6.0_7, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gconf2-3.2.6_5, gdbm-1.13_1, gdk-pixbuf2-2.36.9, geoclue-2.4.3, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glib-networking-2.50.0, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, graphite2-1.3.10, gsettings-desktop-schemas-3.18.1, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_8,3, gstreamer1-1.12.3, gstreamer1-plugins-1.12.3, gtk-update-icon-cache-2.24.29, gtk2-2.24.31, harfbuzz-1.5.1_1, harfbuzz-icu-1.5.1_2, hicolor-icon-theme-0.15, hunspell-1.6.2, icu-59.1,1, indexinfo-0.2.6, inputproto-2.3.2, iso-codes-3.76, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.2, json-glib-1.2.8, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libIDL-0.8.14_3, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_4, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXv-1.0.11,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.83,1, libffi-3.2.1_1, libfontenc-1.1.3_1, libgcrypt-1.8.1, libgpg-error-1.27, libiconv-1.14_11, libidn2-2.0.4, libmspack-0.5, libnghttp2-1.26.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libproxy-0.4.12, libpthread-stubs-0.4, libsecret-0.18.5, libsoup-2.52.2_1, libtasn1-4.12, libunistring-0.9.7, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, libxslt-1.1.29_1, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.3, nspr-4.17, orc-0.4.25, p11-kit-0.23.9, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, png-1.6.34, polkit-0.113_5, py27-setuptools-36.5.0, py27-wxPython-common-3.0.2.0_4, py27-wxPython30-3.0.2.0_4, python2-2_3, python27-2.7.14_1, randrproto-1.5.0, readline-7.0.3, renderproto-0.11.1, shared-mime-info-1.8, spidermonkey170-17.0.0_7, sqlite3-3.20.1_1, tiff-4.0.8, tpm-emulator-0.7.4_2, trousers-0.3.14_1, videoproto-2.3.3, webkit-gtk2-2.4.11_13, webp-0.6.0_4, wx30-gtk2-3.0.2_7, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Deskutils, Python

diamond-0.9.10
BLAST-compatible local sequence aligner
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.32.1, cmake-3.9.4, curl-7.56.0, expat-2.2.1, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, jsoncpp-1.8.1_2, libarchive-3.3.1,1, libffi-3.2.1_1, liblz4-1.8.0,1, libnghttp2-1.26.0, libuv-1.15.0, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.14_1, readline-7.0.3, rhash-1.3.4

emboss-6.6.0_3
Collection of open source tools for genetic sequence analysis
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: clustalw-2.1_1, expat-2.2.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, gmake-4.2.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libgd-2.2.4_1,1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, open-motif-2.3.7, png-1.6.34, primer3-2.3.6, printproto-1.0.5, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.31

fasta-21.1.1
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

fasta3-36.3.8
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: wendell@bsd.com.br

fastdnaml-1.2.2_2
Faster DNAML, makes phylogenetic trees using maximum likelihood
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

fastool-0.1.4
Simple and quick FastQ and FastA tool for file reading and conversion
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com

fastx_toolkit-0.0.14
CLI tools for Short-Reads FASTA/FASTQ files preprocessing
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, indexinfo-0.2.6, libgtextutils-0.7, libtool-2.4.6, m4-1.4.18,1, perl5-5.24.3, pkgconf-1.3.10,1

fluctuate-1.40
Program to fit population models
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

garlic-1.6_1
Molecular viewer, editor, and visualization program
Long description | Changes | Main Web Site
Maintained by: maho@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, kbproto-1.0.7, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, xproto-7.0.31

gff2ps-0.98d_2
Converts gff-formated genomic data-sets to PostScript
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-4.4.12_2, gawk-4.1.4_1, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, libsigsegv-2.11, readline-7.0.3

gmap-2015.09.21
Genomic Mapping and Alignment Program for mRNA and EST Sequences
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, perl5-5.24.3

gperiodic-2.0.10_8
Displays a periodic table of the elements
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-2.24.0, avahi-app-0.6.31_5, ca_root_nss-3.32.1, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.3, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gdbm-1.13_1, gdk-pixbuf2-2.36.9, gettext-runtime-0.19.8.1_1, gettext-tools-0.19.8.1, glib-2.50.2_6,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, graphite2-1.3.10, gtk-update-icon-cache-2.24.29, gtk2-2.24.31, harfbuzz-1.5.1_1, hicolor-icon-theme-0.15, indexinfo-0.2.6, inputproto-2.3.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_4, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.83,1, libffi-3.2.1_1, libfontenc-1.1.3_1, libiconv-1.14_11, libidn2-2.0.4, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.12, libunistring-0.9.7, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.3, p11-kit-0.23.9, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, python2-2_3, python27-2.7.14_1, randrproto-1.5.0, readline-7.0.3, renderproto-0.11.1, shared-mime-info-1.8, tiff-4.0.8, tpm-emulator-0.7.4_2, trousers-0.3.14_1, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6

hmmer-3.0_1
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: perl5-5.24.3

htslib-1.3.1
C library for high-throughput sequencing data formats
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, ca_root_nss-3.32.1, curl-7.56.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libnghttp2-1.26.0, m4-1.4.18,1, perl5-5.24.3
Also listed in: Devel

io_lib-1.14.9
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, ca_root_nss-3.32.1, curl-7.56.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libnghttp2-1.26.0, libtool-2.4.6, m4-1.4.18,1, perl5-5.24.3

iqtree-1.6.b4_1
Efficient phylogenomic software by maximum likelihood
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.28,1, ca_root_nss-3.32.1, cmake-3.9.4, curl-7.56.0, eigen-3.3.4, expat-2.2.1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, jsoncpp-1.8.1_2, libarchive-3.3.1,1, libffi-3.2.1_1, liblz4-1.8.0,1, libnghttp2-1.26.0, libuv-1.15.0, lzo2-2.10_1, mpc-1.0.3, mpfr-3.1.6, ninja-1.8.2,2, python27-2.7.14_1, readline-7.0.3, rhash-1.3.4

jalview-2.07_2
Viewer and editor for multiple sequence alignments
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.1.2, apache-ant-1.9.7, dejavu-2.37, expat-2.2.1, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.8, giflib-5.1.4, inputproto-2.3.2, java-zoneinfo-2017.b, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.144.1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
Also listed in: Java

jellyfish-2.2.6_2
Fast, memory-efficient counting of k-mers in DNA
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libedit-3.1.20170329_2,1, libffi-3.2.1_1, libtool-2.4.6, libunwind-20170113_1, libyaml-0.1.6_2, m4-1.4.18,1, perl5-5.24.3, pkgconf-1.3.10,1, ruby-2.3.5,1, yaggo-1.5.9

lagan-2.0_1
Efficient tools for large-scale multiple alignments of genomic DNA
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.24.3

lamarc-2.1.8_1
Package of programs for computing population parameters
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

libgtextutils-0.7
Gordon's text utilities
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, indexinfo-0.2.6, libtool-2.4.6, m4-1.4.18,1, perl5-5.24.3, pkgconf-1.3.10,1

libsbml-5.15.0
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.32.1, cmake-3.9.4, curl-7.56.0, expat-2.2.1, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, jsoncpp-1.8.1_2, libarchive-3.3.1,1, libffi-3.2.1_1, liblz4-1.8.0,1, libnghttp2-1.26.0, libuv-1.15.0, libxml2-2.9.4, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.14_1, readline-7.0.3, rhash-1.3.4
Also listed in: Devel

linux-foldingathome-5.04
Distributed client for Protein Folding
Long description | Changes | Main Web Site
Maintained by: onatan@gmail.com
Requires: linux_base-c6-6.9_3

mafft-7.266
Multiple alignment program for amino acid or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6

mapm3-3.0
Constructs linkage maps of markers segregating in experimental crosses
Long description | Changes | Main Web Site
Maintained by: tphilipp@potion-studios.com

migrate-3.6.11
Program to estimate population sizes and migration rates
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

minc2-2.2.00_6
Medical Imaging NetCDF
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, bash-4.4.12_2, bison-3.0.4,1, ca_root_nss-3.32.1, curl-7.56.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.2.6, libnghttp2-1.26.0, libtool-2.4.6, m4-1.4.18,1, netcdf-4.5.0, perl5-5.24.3, pkgconf-1.3.10,1
Also listed in: Science

molden-5.7_12
Display molecular orbitals and electron densities in 2D and 3D
Long description | Changes | Main Web Site
Maintained by: jmd@FreeBSD.org
Requires: binutils-2.28,1, damageproto-1.2.1, dri2proto-2.8, dri3proto-1.0, expat-2.2.1, fixesproto-5.0, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, glproto-1.4.17, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, kbproto-1.0.7, libGLU-9.0.0_3, libX11-1.6.5,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mpc-1.0.3, mpfr-3.1.6, pciids-20171011, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.31

mopac-7.1.15_3
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

mrbayes-3.1.2_2
Bayesian inference of phylogeny
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, readline-7.0.3

mummer-3.23_1
Modular system for rapid whole genome alignment
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, perl5-5.24.3

muscle-3.8.31
MUltiple Sequence Comparison by Log-Expectation
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

ncbi-blast-2.5.0_2
NCBI implementation of Basic Local Alignment Search Tool
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, p5-Exporter-Tiny-1.000000, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, pcre-8.40_1, perl5-5.24.3, python27-2.7.14_1, readline-7.0.3

ncbi-toolkit-2012.06.20_1
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.2.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, open-motif-2.3.7, png-1.6.34, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.31

njplot-2.4
Phylogenetic tree drawing program
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: expat-2.2.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, ncbi-toolkit-2012.06.20_1, open-motif-2.3.7, png-1.6.34, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.31

p5-AcePerl-1.92_5
Perl5 interface to the ACEDB genome database system
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Cache-2.11, p5-Cache-Cache-1.08, p5-Digest-SHA1-2.13_1, p5-Error-0.17025, p5-File-NFSLock-1.21_1, p5-Heap-0.80_1, p5-IO-String-1.08_1, p5-IPC-ShareLite-0.17_1, p5-TimeDate-2.30_2,1, perl5-5.24.3
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.72_1
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-Coordinate-1.007001
Modules for working with biological coordinates
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-Das-1.17_4
Client-side library for Distributed Genome Annotation System
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-Das-Lite-2.11_1
Perl extension for the DAS (HTTP+XML) Protocol
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.32.1, curl-7.56.0, libnghttp2-1.26.0, p5-Authen-NTLM-1.09_1, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-File-Listing-6.04_1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-LWP-MediaTypes-6.02_1, p5-Module-Build-0.4224, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-Readonly-2.05, p5-Try-Tiny-0.28, p5-URI-1.72, p5-WWW-Curl-4.17_2, p5-WWW-RobotRules-6.02_1, p5-libwww-6.27, perl5-5.24.3
Also listed in: Perl5

p5-Bio-FeatureIO-1.6.905
Handler for FeatureIO
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-GFF3-2.0_2
Fast low-level functions for parsing and formatting GFF3
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Exporter-Tiny-1.000000, p5-File-ReadBackwards-1.05_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-URI-1.72, perl5-5.24.3
Also listed in: Perl5

p5-Bio-Glite-0.10_2
Perl Interface to G-language
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Authen-NTLM-1.09_1, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-File-Listing-6.04_1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-LWP-MediaTypes-6.02_1, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-Try-Tiny-0.28, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-libwww-6.27, perl5-5.24.3
Also listed in: Perl5

p5-Bio-Graphics-2.40_2
Generate GD Images of Bio::Seq Objects
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.32.1, cairo-1.14.8_1,2, curl-7.56.0, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, io_lib-1.14.9, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libnghttp2-1.26.0, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-Bio-Coordinate-1.007001, p5-Bio-SCF-1.03_1, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.66, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Build-0.4224, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-MAGETAB-1.31_1
Data model and utility API for the MAGE-TAB format
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Algorithm-C3-0.10_1, p5-B-Hooks-EndOfScope-0.21, p5-Carp-Clan-6.06, p5-Class-C3-0.33, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.32, p5-Class-Load-0.24, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.12, p5-Class-Singleton-1.5_1, p5-Data-OptList-0.110, p5-Date-Manip-6.60, p5-DateTime-1.44, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-1.16, p5-DateTime-TimeZone-2.13,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.004, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Email-Valid-1.200, p5-Eval-Closure-0.14, p5-Exception-Class-1.43, p5-File-ShareDir-1.104, p5-IO-Socket-IP-0.39, p5-MRO-Compat-0.13, p5-Mail-Tools-2.14, p5-Module-Implementation-0.09_1, p5-Module-Runtime-0.016, p5-Module-Runtime-Conflicts-0.003_1, p5-Moose-2.2006,1, p5-MooseX-FollowPBP-0.05_1, p5-MooseX-Types-0.50, p5-Net-DNS-1.13,1, p5-Net-Domain-TLD-1.74, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.37_1, p5-Package-Stash-XS-0.28_2, p5-Params-Coerce-0.14_2, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.24, p5-Parse-RecDescent-1.967.009_2, p5-Role-Tiny-2.000005, p5-Scalar-List-Utils-1.48,1, p5-Specio-0.40, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-ForMethods-0.100052, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Identify-0.14, p5-Sub-Install-0.928_1, p5-Sub-Name-0.21,1, p5-Sub-Quote-2.004000, p5-Text-CSV_XS-1.18, p5-TimeDate-2.30_2,1, p5-Try-Tiny-0.28, p5-URI-1.72, p5-Variable-Magic-0.61, p5-namespace-autoclean-0.28, p5-namespace-clean-0.27, perl5-5.24.3
Also listed in: Perl5

p5-Bio-NEXUS-0.78_1
Object-oriented Perl API for the NEXUS file format
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Clone-PP-1.07, perl5-5.24.3
Also listed in: Perl5

p5-Bio-Phylo-0.58_1
Phylogenetic analysis using Perl
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Data-TemporaryBag-0.09_1, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-Font-TTF-1.06, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Bezier-Convert-0.02_1, p5-Math-CDF-0.1_2, p5-Math-Derivative-1.01, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-PDF-API2-2.033, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-SWF-Builder-0.16_2, p5-SWF-File-0.42_2,1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XML2JSON-0.06_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-YAML-Syck-1.27_1, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-SCF-1.03_1
Read and Update SCF Chromatographic Sequence Files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: ca_root_nss-3.32.1, curl-7.56.0, io_lib-1.14.9, libnghttp2-1.26.0, perl5-5.24.3
Also listed in: Perl5

p5-BioPerl-1.007002
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Build-0.4224, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-BioPerl-Run-1.007002
Wrapper modules for common bioinformatics tools
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, graphite2-1.3.10, graphviz-2.40.1_2, harfbuzz-1.5.1_1, indexinfo-0.2.6, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libedit-3.1.20170329_2,1, libevent-2.1.8, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.0,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.38, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.0, p5-Authen-NTLM-1.09_1, p5-Bio-FeatureIO-1.6.905, p5-BioPerl-1.007002, p5-CGI-4.36, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Config-Any-0.32, p5-Config-General-2.63, p5-Config-Tiny-2.23, p5-Convert-Binary-C-0.78, p5-Cpanel-JSON-XS-3.0239, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.043, p5-DBI-1.637, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.02, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17025, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-File-Sort-1.01_1, p5-GD-2.66, p5-Graph-0.96_2,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.13, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.051, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.96, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.426, p5-List-MoreUtils-XS-0.426, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Build-0.4224, p5-Module-Pluggable-5.2, p5-Module-Runtime-0.016, p5-Moo-2.003002, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.17, p5-Net-SSLeay-1.81, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.116, p5-Role-Tiny-2.000005, p5-SVG-2.78, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.48,1, p5-Set-Scalar-1.26_1, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.004000, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.29, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002001, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.72, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0129,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.24, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.65, p5-common-sense-3.74, p5-libwww-6.27, p5-libxml-0.08_1, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, printproto-1.0.5, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, tiff-4.0.8, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-transdecoder-2.1.0
Identify candidate coding regions within transcript sequences
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.28,1, cd-hit-4.6.6_2, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6, p5-URI-1.72, perl5-5.24.3
Also listed in: Perl5

paml-4.9c_1
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6

phrap-1.090518
Phrap is a program for assembling shotgun DNA sequence data
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

phred-0.020425.c
Base calling and quality value assignment on DNA sequencing
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

phylip-3.696
Phylogeny Inference Package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-4.4.12_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXt-1.1.5,1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, printproto-1.0.5, xextproto-7.3.0, xproto-7.0.31

phyml-3.3.20170530
Simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, indexinfo-0.2.6, libtool-2.4.6, m4-1.4.18,1, perl5-5.24.3, pkgconf-1.3.10,1

plink-1.07_7
Whole genome association analysis toolset
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.28,1, blas-3.5.0_3, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, lapack-3.5.0_3, mpc-1.0.3, mpfr-3.1.6
Also listed in: Science

plinkseq-0.10_1
Toolset for working with human genetic variation data
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6
Also listed in: Science

primer3-2.3.6
Primer3 helps to choose primers for PCR reactions
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6

protomol-2.0.3_13
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: damageproto-1.2.1, expat-2.2.1, fixesproto-5.0, freeglut-3.0.0_1, inputproto-2.3.2, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, pciids-20171011, png-1.6.34, randrproto-1.5.0, renderproto-0.11.1, tiff-4.0.8, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.31

psi88-1.0_11
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

py27-biom-format-2.1.6
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.28,1, blas-3.5.0_3, cblas-1.0_7, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.2.6, lapack-3.5.0_3, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, openblas-0.2.20_1,1, perl5-5.24.3, postgresql95-client-9.5.9, py27-click-6.7, py27-future-0.16.0, py27-h5py-2.7.0, py27-numpy-1.13.3,1, py27-pyqi-0.3.2, py27-scipy-0.19.0_3, py27-setuptools-36.5.0, py27-six-1.11.0, python27-2.7.14_1, readline-7.0.3, suitesparse-4.0.2_7, swig13-1.3.40_1
Also listed in: Python

py27-biopython-1.70
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: binutils-2.28,1, blas-3.5.0_3, cblas-1.0_7, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, lapack-3.5.0_3, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, openblas-0.2.20_1,1, py27-numpy-1.13.3,1, py27-reportlab1-1.21.2_3, py27-setuptools-36.5.0, python2-2_3, python27-2.7.14_1, readline-7.0.3, suitesparse-4.0.2_7
Also listed in: Python

py27-bx-python-0.7.4
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@rawbw.com
Requires: binutils-2.28,1, blas-3.5.0_3, cblas-1.0_7, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, lapack-3.5.0_3, libffi-3.2.1_1, lzo2-2.10_1, mpc-1.0.3, mpfr-3.1.6, openblas-0.2.20_1,1, py27-numpy-1.13.3,1, py27-python-lzo-1.11, py27-setuptools-36.5.0, python2-2_3, python27-2.7.14_1, readline-7.0.3, suitesparse-4.0.2_7
Also listed in: Python

py27-pysam-0.11.2.2
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@rawbw.com
Requires: cython-0.26, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libffi-3.2.1_1, py27-setuptools-36.5.0, python27-2.7.14_1, readline-7.0.3
Also listed in: Python

pycogent-1.9
Toolkit for statistical analysis of biological sequences
Long description | Changes | Main Web Site
Maintained by: python@FreeBSD.org
Requires: binutils-2.28,1, blas-3.5.0_3, ca_root_nss-3.32.1, cblas-1.0_7, cython-0.26, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, lapack-3.5.0_3, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, openblas-0.2.20_1,1, py27-Babel-2.3.4, py27-Jinja2-2.9.5, py27-MarkupSafe-1.0, py27-alabaster-0.7.6, py27-docutils-0.14, py27-imagesize-0.7.1, py27-numpy-1.13.3,1, py27-pygments-2.2.0, py27-pystemmer-1.3.0_1, py27-pytz-2017.2,1, py27-setuptools-36.5.0, py27-six-1.11.0, py27-snowballstemmer-1.2.0_1, py27-sphinx-1.4.8_2,1, py27-sphinx_rtd_theme-0.2.4, py27-sqlalchemy10-1.0.14, py27-sqlite3-2.7.14_7, python27-2.7.14_1, readline-7.0.3, sqlite3-3.20.1_1, suitesparse-4.0.2_7
Also listed in: Python

pyfasta-0.5.2_1
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: binutils-2.28,1, blas-3.5.0_3, cblas-1.0_7, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, lapack-3.5.0_3, libffi-3.2.1_1, mpc-1.0.3, mpfr-3.1.6, openblas-0.2.20_1,1, py27-numpy-1.13.3,1, py27-setuptools-36.5.0, python27-2.7.14_1, readline-7.0.3, suitesparse-4.0.2_7
Also listed in: Python

python-nexus-1.53
Generic nexus file format reader for python
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, indexinfo-0.2.6, libffi-3.2.1_1, py27-setuptools-36.5.0, python27-2.7.14_1, readline-7.0.3
Also listed in: Python

raster3d-3.0.2_10
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ImageMagick-6.9.9.15,1, avahi-app-0.6.31_5, binutils-2.28,1, ca_root_nss-3.32.1, cairo-1.14.8_1,2, cups-2.2.3, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fftw3-3.3.6.p2_2, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gcc-ecj-4.5, gcc6-6.4.0_2, gdbm-1.13_1, gdk-pixbuf2-2.36.9, gettext-runtime-0.19.8.1_1, ghostscript9-agpl-base-9.16_5, ghostscript9-agpl-x11-9.16_2, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, graphite2-1.3.10, gsfonts-8.11_8, harfbuzz-1.5.1_1, indexinfo-0.2.6, inputproto-2.3.2, jasper-1.900.1_17, jbig2dec-0.14, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, lcms2-2.8, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libcroco-0.6.11, libdaemon-0.14_1, libdrm-2.4.83,1, libffi-3.2.1_1, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libgsf-1.14.41, libiconv-1.14_11, libidn-1.33_1, libidn2-2.0.4, liblqr-1-0.4.2, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libraw-0.18.5, librsvg2-2.40.17, libtasn1-4.12, libunistring-0.9.7, libunwind-20170113_1, libwmf-0.2.8.4_15, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpfr-3.1.6, nettle-3.3, openjpeg-2.3.0, p11-kit-0.23.9, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, python2-2_3, python27-2.7.14_1, readline-7.0.3, renderproto-0.11.1, shared-mime-info-1.8, svgalib-1.4.3_7, tiff-4.0.8, tpm-emulator-0.7.4_2, trousers-0.3.14_1, webp-0.6.0_4, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Graphics

recombine-1.41
Program to fit population models across sites
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

ruby23-bio-1.5.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: indexinfo-0.2.6, libedit-3.1.20170329_2,1, libffi-3.2.1_1, libunwind-20170113_1, libyaml-0.1.6_2, ruby-2.3.5,1
Also listed in: Ruby

rubygem-bio-1.5.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: ruby@FreeBSD.org
Requires: indexinfo-0.2.6, libedit-3.1.20170329_2,1, libffi-3.2.1_1, libunwind-20170113_1, libyaml-0.1.6_2, ruby-2.3.5,1, ruby23-gems-2.6.14
Also listed in: Rubygems

samtools-1.3.1
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, ca_root_nss-3.32.1, curl-7.56.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, htslib-1.3.1, indexinfo-0.2.6, libnghttp2-1.26.0, m4-1.4.18,1, perl5-5.24.3

seaview-4.6.2
Multiple DNA/protein sequence alignment editor
Long description | Changes | Main Web Site
Maintained by: bofh@FreeBSD.org
Requires: damageproto-1.2.1, expat-2.2.1, fixesproto-5.0, fltk-1.3.4, fontconfig-2.12.1,1, freetype2-2.8, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, jpeg-turbo-1.5.2, kbproto-1.0.7, libGLU-9.0.0_3, libX11-1.6.5,1, libXau-1.0.8_3, libXcursor-1.1.14_4, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXinerama-1.1.3_3,1, libXrender-0.9.10, libXxf86vm-1.1.4_1, libdrm-2.4.83,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, pciids-20171011, png-1.6.34, renderproto-0.11.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.31

seqan-2.2.0
C++ Sequence Analysis Template Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqan-apps-2.2.0_8
Official Bioinformatic applications based on the SeqAn library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: binutils-2.28,1, boost-libs-1.65.1, ca_root_nss-3.32.1, cmake-3.9.4, curl-7.56.0, expat-2.2.1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, icu-59.1,1, indexinfo-0.2.6, jsoncpp-1.8.1_2, libarchive-3.3.1,1, libffi-3.2.1_1, liblz4-1.8.0,1, libnghttp2-1.26.0, libuv-1.15.0, lzo2-2.10_1, mpc-1.0.3, mpfr-3.1.6, ninja-1.8.2,2, python27-2.7.14_1, readline-7.0.3, rhash-1.3.4

seqan1-1.3.1_4
C++ Sequence Analysis Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqio-1.2.2_1
Set of C functions which can read/write biological sequence files
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

seqtools-4.44.1_2
Tools for visualising sequence alignments
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: atk-2.24.0, avahi-app-0.6.31_5, ca_root_nss-3.32.1, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.3, curl-7.56.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.1,1, freetype2-2.8, gdbm-1.13_1, gdk-pixbuf2-2.36.9, gettext-runtime-0.19.8.1_1, gettext-tools-0.19.8.1, glib-2.50.2_6,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, graphite2-1.3.10, gtk-update-icon-cache-2.24.29, gtk2-2.24.31, harfbuzz-1.5.1_1, hicolor-icon-theme-0.15, indexinfo-0.2.6, inputproto-2.3.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_4, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.83,1, libffi-3.2.1_1, libfontenc-1.1.3_1, libiconv-1.14_11, libidn2-2.0.4, libnghttp2-1.26.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.12, libunistring-0.9.7, libunwind-20170113_1, libxcb-1.12_2, libxml2-2.9.4, libxshmfence-1.2_2, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.3, p11-kit-0.23.9, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, pkgconf-1.3.10,1, png-1.6.34, python2-2_3, python27-2.7.14_1, randrproto-1.5.0, readline-7.0.3, renderproto-0.11.1, shared-mime-info-1.8, sqlite3-3.20.1_1, tiff-4.0.8, tpm-emulator-0.7.4_2, trousers-0.3.14_1, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31

sim4-2003.09.21_1
Algorithm for aligning expressed DNA with genomic sequences
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

slclust-2010.02.02
Single-linkage clustering with Jaccard similarity
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com

ssaha-3.1c_5
Very fast matching and alignment of DNA sequences
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

tRNAscan-SE-1.23_1
Improved tool for transfer RNA detection
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.24.3

t_coffee-9.03_6
Multiple DNA or protein sequence alignment package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.28,1, clustalw-2.1_1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

tinker-7.1.3_3
General purpose molecular modelling package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.28,1, gcc-ecj-4.5, gcc6-6.4.0_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.2.6, mpc-1.0.3, mpfr-3.1.6

treepuzzle-5.2
Maximum likelihood phylogeny reconstruction using quartets
Long description | Changes | Main Web Site
Maintained by: jan.lentfer@web.de

trimmomatic-0.35
Flexible read trimming tool for Illumina NGS data
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: alsa-lib-1.1.2, dejavu-2.37, expat-2.2.1, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.8, giflib-5.1.4, inputproto-2.3.2, java-zoneinfo-2017.b, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.144.1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
Also listed in: Java

ugene-1.22.0_2
Free, open-source, cross-platform bioinformatics toolkit
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: avahi-app-0.6.31_5, bash-4.4.12_2, ca_root_nss-3.32.1, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.3, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, desktop-file-utils-0.23, dri2proto-2.8, dri3proto-1.0, encodings-1.0.4_3,1, expat-2.2.1, ffmpeg-3.4,1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontcacheproto-0.1.3, fontconfig-2.12.1,1, freetype2-2.8, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.2_6,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.15, gobject-introspection-1.50.0,1, graphite2-1.3.10, gstreamer1-1.12.3, gstreamer1-libav-1.12.3_1, gstreamer1-plugins-1.12.3, gstreamer1-plugins-a52dec-1.12.3, gstreamer1-plugins-bad-1.12.3, gstreamer1-plugins-core-1.12, gstreamer1-plugins-dts-1.12.3, gstreamer1-plugins-dvdread-1.12.3, gstreamer1-plugins-good-1.12.3, gstreamer1-plugins-mpg123-1.12.3, gstreamer1-plugins-ogg-1.12.3, gstreamer1-plugins-pango-1.12.3, gstreamer1-plugins-png-1.12.3, gstreamer1-plugins-resindvd-1.12.3, gstreamer1-plugins-theora-1.12.3, gstreamer1-plugins-ugly-1.12.3, gstreamer1-plugins-vorbis-1.12.3, harfbuzz-1.5.1_1, hicolor-icon-theme-0.15, hyphen-2.8.8, icu-59.1,1, indexinfo-0.2.6, inputproto-2.3.2, iso-codes-3.76, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.2, kbproto-1.0.7, lcms-1.19_6,1, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXfontcache-1.0.5_3, libXft-2.3.2_1, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, liba52-0.7.4_3, libdaemon-0.14_1, libdca-0.0.5_1, libdrm-2.4.83,1, libdvdcss-1.4.0_1, libdvdnav-5.0.3, libdvdread-5.0.3, libffi-3.2.1_1, libfontenc-1.1.3_1, libgcrypt-1.8.1, libgpg-error-1.27, libiconv-1.14_11, libidn2-2.0.4, libltdl-2.4.6, libmng-1.0.10_3, libogg-1.3.2_2,4, libpaper-1.1.24.4, libpciaccess-0.13.5, libproxy-0.4.12, libpthread-stubs-0.4, libtasn1-4.12, libtheora-1.1.1_7, libunistring-0.9.7, libunwind-20170113_1, libv4l-1.6.3_2, libva-1.8.3, libvdpau-1.1.1, libvorbis-1.3.5_1,3, libvpx-1.6.1_2, libx264-0.148.2795, libxcb-1.12_2, libxkbcommon-0.7.1_1, libxml2-2.9.4, libxshmfence-1.2_2, libxslt-1.1.29_1, mesa-libs-17.2.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mpg123-1.25.7, nettle-3.3, opencv-core-2.4.13.1_1, orc-0.4.25, p11-kit-0.23.9, pango-1.40.6, pciids-20171011, pcre-8.40_1, perl5-5.24.3, pixman-0.34.0, png-1.6.34, python2-2_3, python27-2.7.14_1, qt5-buildtools-5.7.1, qt5-core-5.7.1_3, qt5-dbus-5.7.1, qt5-gui-5.7.1_1, qt5-imageformats-5.7.1_1, qt5-linguisttools-5.7.1, qt5-location-5.7.1, qt5-network-5.7.1_1, qt5-opengl-5.7.1_1, qt5-printsupport-5.7.1, qt5-qmake-5.7.1_5, qt5-qml-5.7.1_1, qt5-quick-5.7.1_1, qt5-script-5.7.1_2, qt5-scripttools-5.7.1, qt5-sensors-5.7.1, qt5-sql-5.7.1, qt5-svg-5.7.1, qt5-testlib-5.7.1, qt5-webchannel-5.7.1, qt5-webkit-5.212.0.a2_2, qt5-widgets-5.7.1, qt5-xml-5.7.1, qt5-xmlpatterns-5.7.1, qtchooser-39, readline-7.0.3, renderproto-0.11.1, sqlite3-3.20.1_1, tiff-4.0.8, tpm-emulator-0.7.4_2, trousers-0.3.14_1, v4l_compat-1.6.3, webp-0.6.0_4, x265-2.3, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xprop-1.2.2, xproto-7.0.31, xset-1.2.3_1, xvid-1.3.4,1
Also listed in: Science

vcftools-0.1.14
Tools for working with VCF genomics files
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.15.1, automake-wrapper-20131203, gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, m4-1.4.18,1, perl5-5.24.3, pkgconf-1.3.10,1

velvet-1.2.10_2
Sequence assembler for very short reads
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_1, indexinfo-0.2.6, libffi-3.2.1_1, perl5-5.24.3, python27-2.7.14_1, readline-7.0.3

wise-2.4.1_1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, glib-2.50.2_6,1, indexinfo-0.2.6, libffi-3.2.1_1, libiconv-1.14_11, pcre-8.40_1, perl5-5.24.3, pkgconf-1.3.10,1, python27-2.7.14_1, readline-7.0.3

xmolwt-0.7_7
Calculate atom weight and percent of each element for a given formula
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: fixesproto-5.0, gettext-runtime-0.19.8.1_1, glib12-1.2.10_15, gmake-4.2.1_1, gtk12-1.2.10_25, indexinfo-0.2.6, inputproto-2.3.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libpthread-stubs-0.4, libxcb-1.12_2, libxml2-2.9.4, xextproto-7.3.0, xproto-7.0.31

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