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FreeBSD Ports: Biology

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Biologie-Software.

FastTree-2.1.8
Approximately-maximum-likelihood phylogenetic trees from alignments
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

InsightToolkit-4.10.0
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@FreeBSD.org
Requires: binutils-2.27_1,1, ca_root_nss-3.26, cmake-3.6.1, cmake-modules-3.6.1, curl-7.50.1, expat-2.2.0, fftw-2.1.5_12, gcc-4.8.5_2, gcc-ecj-4.5, gdcm-2.6.3_1, gettext-runtime-0.19.8.1, gmp-5.1.3_3, hdf-szip-2.1_2, hdf5-1.10.0, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, jsoncpp-1.7.3, lcms2-2.7_2, libarchive-3.2.1,1, liblz4-131, lzo2-2.09, mpc-1.0.3, mpfr-3.1.4, openjpeg15-1.5.2_1, png-1.6.23, tiff-4.0.6_2
Also listed in: Science

afni-2015.11.13
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: R-3.3.1_3, avahi-app-0.6.31_5, binutils-2.27_1,1, ca_root_nss-3.26, cairo-1.14.6_1,2, cups-2.1.4, curl-7.50.1, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, endian-1.1, expat-2.2.0, f2c-20060810_4, 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, freetype2-2.6.3, gbm-11.2.2, gcc-4.8.5_2, gcc-ecj-4.5, gdbm-1.12, gettext-runtime-0.19.8.1, gettext-tools-0.19.8.1, ghostscript9-agpl-base-9.16_5, glib-2.46.2_2, glproto-1.4.17, gmake-4.2.1_1, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gsfonts-8.11_6, gsl-1.16_2, harfbuzz-1.3.0, hdf-szip-2.1_2, hdf5-1.10.0, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, jasper-1.900.1_16, jbig2dec-0.13, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, lcms2-2.7_2, libEGL-11.2.2, libGL-11.2.2, libGLU-9.0.0_2, libGLw-8.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXi-1.7.6,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libglapi-11.2.2, libiconv-1.14_9, libidn-1.33_1, libpaper-1.1.24.4, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libtasn1-4.9, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, m4-1.4.17_1,1, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpeg_encode-1.5b, mpfr-3.1.4, netcdf-4.4.0_2, netcdf-fortran-4.4.4, netpbm-10.35.98, nettle-3.2, open-motif-2.3.6_1, p11-kit-0.23.2, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, pkgconf-1.0.1, png-1.6.23, printproto-1.0.5, python2-2_3, python27-2.7.12, qhull5-1.0_3, renderproto-0.11.1, scrnsaverproto-1.2.2, svgalib-1.4.3_7, tcl86-8.6.6, tiff-4.0.6_2, tk86-8.6.6, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, xbitmaps-1.1.1, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
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, gmake-4.2.1_1, indexinfo-0.2.4

artemis-9_1
DNA sequence viewer and annotation tool
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.1.2, dejavu-2.35, expat-2.2.0, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.6.3, giflib-5.1.3, inputproto-2.3.1, java-zoneinfo-2016.f, javavmwrapper-2.5_2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.6,1, libXrender-0.9.9, libXt-1.1.5,1, libXtst-1.2.2_3, libfontenc-1.1.3, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.102.14, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.28
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-3.26, cmake-3.6.1, cmake-modules-3.6.1, curl-7.50.1, expat-2.2.0, jsoncpp-1.7.3, libarchive-3.2.1,1, liblz4-131, lzo2-2.09

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
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: ca_root_nss-3.26, curl-7.50.1, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gsl-1.16_2, htslib-1.3.1, indexinfo-0.2.4

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, gmake-4.2.1_1, indexinfo-0.2.4, libffi-3.2.1, python27-2.7.12

biococoa-2.2.2_2
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: theraven@FreeBSD.org
Requires: avahi-app-0.6.31_5, ca_root_nss-3.26, cairo-1.14.6_1,2, cups-2.1.4, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dri2proto-2.8, expat-2.2.0, fixesproto-5.0, flac-1.3.1_2, fontconfig-2.12.1,1, freetype2-2.6.3, gbm-11.2.2, gdbm-1.12, gettext-runtime-0.19.8.1, giflib-5.1.3, glib-2.46.2_2, glproto-1.4.17, gmake-4.2.1_1, gmp-5.1.3_3, gnome_subr-1.0, gnustep-back-0.24.1, gnustep-base-1.24.8_4, gnustep-gui-0.24.1_3, gnustep-make-2.6.7_2, gnutls-3.4.14, gobject-introspection-1.46.0, icu-55.1,1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libGLU-9.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXcursor-1.1.14_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libao-1.2.0_3, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libgcrypt-1.7.3, libglapi-11.2.2, libgpg-error-1.24, libiconv-1.14_9, libidn-1.33_1, libobjc2-1.8.1, libogg-1.3.2_1,4, libpaper-1.1.24.4, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libsndfile-1.0.26, libtasn1-4.9, libvorbis-1.3.5,3, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, libxslt-1.1.29, llvm37-3.7.1_3, nettle-3.2, p11-kit-0.23.2, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, python2-2_3, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.28
Also listed in: Gnustep

biojava-1.7
Open-source Java tools for processing biological data
Long description | Changes | Main Web Site
Maintained by: wenheping@gmail.com
Requires: alsa-lib-1.1.2, apache-ant-1.9.7, dejavu-2.35, expat-2.2.0, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.6.3, giflib-5.1.3, inputproto-2.3.1, java-zoneinfo-2016.f, javavmwrapper-2.5_2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.6,1, libXrender-0.9.9, libXt-1.1.5,1, libXtst-1.2.2_3, libfontenc-1.1.3, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.102.14, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.28
Also listed in: Java

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, gmake-4.2.1_1, indexinfo-0.2.4, libedit-3.1.20150325_2,1, mysql56-client-5.6.30, png-1.6.23

bowtie-1.1.2
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4, perl5-5.20.3_15

bowtie2-2.2.8
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4, perl5-5.20.3_15

bwa-0.7.9a
Burrows-Wheeler sequence aligner
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: perl5-5.20.3_15

cd-hit-4.6.4
Clustering and comparing protein or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

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, gmake-4.2.1_1, indexinfo-0.2.4

chemeq-1.50_2
Outputs LaTeX code for chemical reaction
Long description | Changes
Maintained by: ports@FreeBSD.org
Requires: bison-2.7.1,1, gettext-runtime-0.19.8.1, indexinfo-0.2.4, m4-1.4.17_1,1
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_2, linux-c6-fontconfig-2.8.0_1, linux-c6-xorg-libs-7.4_5, linux_base-c6-6.8, perl5-5.20.3_15, phrap-1.090518, phred-0.020425.c

crux-1.2.0_5
Software toolkit for phylogenetic inference
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.4, python27-2.7.12
Also listed in: Python

cycle-0.3.1_9
Calendar program for women
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_1, atk-2.18.0, avahi-app-0.6.31_5, ca_root_nss-3.26, cairo-1.14.6_1,2, cantarell-fonts-0.0.24, compositeproto-0.4.2, cups-2.1.4, curl-7.50.1, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dconf-0.24.0_1, dejavu-2.35, dri2proto-2.8, enchant-1.6.0_5, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gconf2-3.2.6_4, gdbm-1.12, gdk-pixbuf2-2.32.3_1, geoclue-2.3.0, gettext-runtime-0.19.8.1, giflib-5.1.3, glib-2.46.2_2, glib-networking-2.46.1_1, glproto-1.4.17, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gsettings-desktop-schemas-3.18.1, gstreamer-0.10.36_4, gstreamer-plugins-0.10.36_6,3, gstreamer1-1.8.0, gstreamer1-plugins-1.8.0, gtk-update-icon-cache-2.24.29, gtk2-2.24.29_2, harfbuzz-1.3.0, hicolor-icon-theme-0.15, hunspell-1.3.3, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, iso-codes-3.69, jasper-1.900.1_16, jbigkit-2.1_1, jpeg-turbo-1.4.2, json-glib-1.1.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libGLU-9.0.0_2, libICE-1.0.9_1,1, libIDL-0.8.14_2, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXi-1.7.6,1, libXinerama-1.1.3_3,1, libXrandr-1.5.0, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgcrypt-1.7.3, libglapi-11.2.2, libgpg-error-1.24, libiconv-1.14_9, libidn-1.33_1, libmspack-0.5, libpaper-1.1.24.4, libpciaccess-0.13.4, libproxy-0.4.12, libpthread-stubs-0.3_6, libsecret-0.18.4, libsoup-2.52.2, libtasn1-4.9, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, libxslt-1.1.29, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.2, nspr-4.12, orc-0.4.25, p11-kit-0.23.2, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, polkit-0.113_1, py27-setuptools27-23.1.0, py27-wxPython-common-3.0.2.0_1, py27-wxPython30-3.0.2.0, python-2.7_2,2, python2-2_3, python27-2.7.12, randrproto-1.5.0, renderproto-0.11.1, shared-mime-info-1.5, spidermonkey170-17.0.0_1, sqlite3-3.14.1, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, webkit-gtk2-2.4.11_3, webp-0.5.0, wx30-gtk2-3.0.2_4, xcb-util-0.4.0_1,1, 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-7.0.28
Also listed in: Deskutils, Python

diamond-0.8.19
BLAST-compatible local sequence aligner
Long description | Changes | Main Web Site
Maintained by: jrm@ftfl.ca
Requires: ca_root_nss-3.26, cmake-3.6.1, cmake-modules-3.6.1, curl-7.50.1, expat-2.2.0, jsoncpp-1.7.3, libarchive-3.2.1,1, liblz4-131, lzo2-2.09

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-2.2.0, fontconfig-2.12.1,1, freetype2-2.6.3, gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libgd-2.2.2,1, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, open-motif-2.3.6_1, png-1.6.23, primer3-2.3.6, printproto-1.0.5, renderproto-0.11.1, tiff-4.0.6_2, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.28

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-0.2.4, libgtextutils-0.7, libtool-2.4.6, m4-1.4.17_1,1, perl5-5.20.3_15, pkgconf-1.0.1

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, gmake-4.2.1_1, indexinfo-0.2.4, kbproto-1.0.7, libX11-1.6.3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, xproto-7.0.28

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-4.3.46_1, gawk-4.1.3_2, gettext-runtime-0.19.8.1, indexinfo-0.2.4, libsigsegv-2.10_1

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, gmake-4.2.1_1, indexinfo-0.2.4, perl5-5.20.3_15

gperiodic-2.0.10_7
Displays a periodic table of the elements
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-2.18.0, avahi-app-0.6.31_5, ca_root_nss-3.26, cairo-1.14.6_1,2, compositeproto-0.4.2, cups-2.1.4, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gdbm-1.12, gdk-pixbuf2-2.32.3_1, gettext-runtime-0.19.8.1, gettext-tools-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gtk-update-icon-cache-2.24.29, gtk2-2.24.29_2, harfbuzz-1.3.0, hicolor-icon-theme-0.15, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, jasper-1.900.1_16, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXi-1.7.6,1, libXinerama-1.1.3_3,1, libXrandr-1.5.0, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libglapi-11.2.2, libiconv-1.14_9, libidn-1.33_1, libpaper-1.1.24.4, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libtasn1-4.9, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.2, p11-kit-0.23.2, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, pkgconf-1.0.1, png-1.6.23, python-2.7_2,2, python2-2_3, python27-2.7.12, randrproto-1.5.0, renderproto-0.11.1, shared-mime-info-1.5, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, xcb-util-0.4.0_1,1, 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-7.0.28

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, gmake-4.2.1_1, indexinfo-0.2.4

hmmer-3.0_1
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: perl5-5.20.3_15

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-3.26, curl-7.50.1, gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4, m4-1.4.17_1,1, perl5-5.20.3_15
Also listed in: Devel

io_lib-1.14.8
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: ca_root_nss-3.26, curl-7.50.1, gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4

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-2.35, expat-2.2.0, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.6.3, giflib-5.1.3, inputproto-2.3.1, java-zoneinfo-2016.f, javavmwrapper-2.5_2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.6,1, libXrender-0.9.9, libXt-1.1.5,1, libXtst-1.2.2_3, libfontenc-1.1.3, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.102.14, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.28
Also listed in: Java

jellyfish-2.2.4
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, gmake-4.2.1_1, indexinfo-0.2.4, libedit-3.1.20150325_2,1, libffi-3.2.1, libtool-2.4.6, libyaml-0.1.6_2, m4-1.4.17_1,1, perl5-5.20.3_15, pkgconf-1.0.1, ruby-2.2.5,1, 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: perl5-5.20.3_15

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-0.2.4, libtool-2.4.6, m4-1.4.17_1,1, perl5-5.20.3_15, pkgconf-1.0.1

libsbml-5.13.0
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.26, cmake-3.6.1, cmake-modules-3.6.1, curl-7.50.1, expat-2.2.0, jsoncpp-1.7.3, libarchive-3.2.1,1, liblz4-131, libxml2-2.9.3, lzo2-2.09
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-c6-6.8

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, gmake-4.2.1_1, indexinfo-0.2.4

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_4
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-4.3.46_1, bison-2.7.1,1, ca_root_nss-3.26, curl-7.50.1, gettext-runtime-0.19.8.1, gmake-4.2.1_1, hdf-szip-2.1_2, hdf5-1.10.0, indexinfo-0.2.4, libtool-2.4.6, m4-1.4.17_1,1, netcdf-4.4.0_2, perl5-5.20.3_15, pkgconf-1.0.1
Also listed in: Science

molden-5.7
Display molecular orbitals and electron densities in 2D and 3D
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: binutils-2.27_1,1, damageproto-1.2.1, dri2proto-2.8, expat-2.2.0, fixesproto-5.0, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, glproto-1.4.17, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, kbproto-1.0.7, libGL-11.2.2, libGLU-9.0.0_2, libX11-1.6.3,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libglapi-11.2.2, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, mpc-1.0.3, mpfr-3.1.4, pciids-20160621, videoproto-2.3.2, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.28

mopac-7.1.15
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

mrbayes-3.1.2_1
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, gmake-4.2.1_1, indexinfo-0.2.4, readline-6.3.8

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, gmake-4.2.1_1, indexinfo-0.2.4, perl5-5.20.3_15

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-2.2.30_2
NCBI implementation of Basic Local Alignment Search Tool
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.27_1,1, bzip2-1.0.6_1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.4, p5-Exporter-Tiny-0.042_1, p5-List-MoreUtils-0.413, pcre-8.39, perl5-5.20.3_15, python27-2.7.12

ncbi-toolkit-2012.06.20
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.2.0, fontconfig-2.12.1,1, freetype2-2.6.3, gettext-runtime-0.19.8.1, indexinfo-0.2.4, jpeg-turbo-1.4.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, open-motif-2.3.6_1, png-1.6.23, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.28

p5-AcePerl-1.92_4
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-0.17024, 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, perl5-5.20.3_15
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.70_1
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.6_1,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, graphite2-1.3.8, graphviz-2.38.0_13, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgd-2.2.2,1, libglapi-11.2.2, libiconv-1.14_9, libltdl-2.4.6, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.30, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.12, p5-Authen-NTLM-1.09_1, p5-Class-AutoClass-1.56_1, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.28_1, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-BinHex-1.125, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.035, p5-DBI-1.636, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17024, p5-Exception-Class-1.40, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_3, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.21, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.13, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.03_1, p5-HTTP-Cookies-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-Hash-AutoHash-1.17_1, p5-Hash-AutoHash-Args-1.18_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-SessionData-1.03_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-IO-String-1.08_1, p5-IO-Tty-1.12_1, p5-IO-stringy-2.111, p5-IPC-Run-0.94, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.507,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.04, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.014_1, p5-Moo-2.002004, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000003, p5-SOAP-Lite-1.20, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.26_1, p5-Socket-2.021, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Install-0.928_1, p5-Sub-Uplevel-0.2500, p5-Task-Weaken-1.04_1, p5-Test-Deep-1.120, p5-Test-Differences-0.630,1, p5-Test-Exception-0.43, p5-Test-Most-0.34_1, p5-Test-Simple-1.302037, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_3, p5-Text-Shellwords-1.08_1, p5-Text-Tabs+Wrap-2013.0523_1, p5-Tie-IxHash-1.23_1, p5-Tie-ToObject-0.03_2, p5-TimeDate-2.30_2,1, p5-Tree-DAG_Node-1.29, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.71, 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-2.0126,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.721, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.08_1, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.56, p5-XML-Simple-2.22, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.37, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-bioperl-1.6.924_4, p5-libwww-6.15, p5-libxml-0.08_1, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, printproto-1.0.5, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
Also listed in: Perl5

p5-Bio-Das-1.17_3
Client-side library for Distributed Genome Annotation System
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.6_1,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, graphite2-1.3.8, graphviz-2.38.0_13, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgd-2.2.2,1, libglapi-11.2.2, libiconv-1.14_9, libltdl-2.4.6, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.30, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.12, p5-Authen-NTLM-1.09_1, p5-Class-AutoClass-1.56_1, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.28_1, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-BinHex-1.125, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.035, p5-DBI-1.636, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17024, p5-Exception-Class-1.40, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_3, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.21, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.13, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.03_1, p5-HTTP-Cookies-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-Hash-AutoHash-1.17_1, p5-Hash-AutoHash-Args-1.18_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-SessionData-1.03_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-IO-String-1.08_1, p5-IO-Tty-1.12_1, p5-IO-stringy-2.111, p5-IPC-Run-0.94, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.507,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.04, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.014_1, p5-Moo-2.002004, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000003, p5-SOAP-Lite-1.20, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.26_1, p5-Socket-2.021, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Install-0.928_1, p5-Sub-Uplevel-0.2500, p5-Task-Weaken-1.04_1, p5-Test-Deep-1.120, p5-Test-Differences-0.630,1, p5-Test-Exception-0.43, p5-Test-Most-0.34_1, p5-Test-Simple-1.302037, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_3, p5-Text-Shellwords-1.08_1, p5-Text-Tabs+Wrap-2013.0523_1, p5-Tie-IxHash-1.23_1, p5-Tie-ToObject-0.03_2, p5-TimeDate-2.30_2,1, p5-Tree-DAG_Node-1.29, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.71, 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-2.0126,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.721, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.08_1, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.56, p5-XML-Simple-2.22, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.37, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-bioperl-1.6.924_4, p5-libwww-6.15, p5-libxml-0.08_1, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, printproto-1.0.5, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
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-3.26, curl-7.50.1, p5-Authen-NTLM-1.09_1, p5-CPAN-Meta-2.150005, 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-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-LWP-MediaTypes-6.02_1, p5-Module-Build-0.4218, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-Readonly-2.05, p5-Socket-2.021, p5-URI-1.71, p5-WWW-Curl-4.17_2, p5-WWW-RobotRules-6.02_1, p5-libwww-6.15, perl5-5.20.3_15
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-0.042_1, p5-File-ReadBackwards-1.05_1, p5-List-MoreUtils-0.413, p5-URI-1.71, perl5-5.20.3_15
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-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-LWP-MediaTypes-6.02_1, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-Socket-2.021, p5-URI-1.71, p5-WWW-RobotRules-6.02_1, p5-libwww-6.15, perl5-5.20.3_15
Also listed in: Perl5

p5-Bio-Graphics-2.39
Generate GD Images of Bio::Seq Objects
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.26, cairo-1.14.6_1,2, curl-7.50.1, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, graphite2-1.3.8, graphviz-2.38.0_13, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, io_lib-1.14.8, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgd-2.2.2,1, libglapi-11.2.2, libiconv-1.14_9, libltdl-2.4.6, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.30, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.12, p5-Authen-NTLM-1.09_1, p5-Bio-SCF-1.03_1, p5-CPAN-Meta-2.150005, p5-Class-AutoClass-1.56_1, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.28_1, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-BinHex-1.125, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.035, p5-DBI-1.636, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17024, p5-Exception-Class-1.40, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_3, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.21, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.13, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.03_1, p5-HTTP-Cookies-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-Hash-AutoHash-1.17_1, p5-Hash-AutoHash-Args-1.18_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-SessionData-1.03_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-IO-String-1.08_1, p5-IO-Tty-1.12_1, p5-IO-stringy-2.111, p5-IPC-Run-0.94, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.507,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.04, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Build-0.4218, p5-Module-Runtime-0.014_1, p5-Moo-2.002004, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000003, p5-SOAP-Lite-1.20, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.26_1, p5-Socket-2.021, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Install-0.928_1, p5-Sub-Uplevel-0.2500, p5-Task-Weaken-1.04_1, p5-Test-Deep-1.120, p5-Test-Differences-0.630,1, p5-Test-Exception-0.43, p5-Test-Most-0.34_1, p5-Test-Simple-1.302037, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_3, p5-Text-Shellwords-1.08_1, p5-Text-Tabs+Wrap-2013.0523_1, p5-Tie-IxHash-1.23_1, p5-Tie-ToObject-0.03_2, p5-TimeDate-2.30_2,1, p5-Tree-DAG_Node-1.29, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.71, 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-2.0126,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.721, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.08_1, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.56, p5-XML-Simple-2.22, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.37, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-bioperl-1.6.924_4, p5-libwww-6.15, p5-libxml-0.08_1, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, printproto-1.0.5, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
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-C3-0.31, p5-Class-Load-0.22, p5-Class-Load-XS-0.09_1, p5-Class-Singleton-1.5_1, p5-Data-OptList-0.110, p5-Date-Manip-6.53, p5-DateTime-1.36_1, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-1.05, p5-DateTime-TimeZone-2.01, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-OverloadInfo-0.004, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Email-Valid-1.192_1, p5-Eval-Closure-0.14, p5-Exporter-Tiny-0.042_1, p5-IO-Socket-IP-0.37_1, p5-List-AllUtils-0.10, p5-List-SomeUtils-0.52, p5-List-SomeUtils-XS-0.52, p5-MRO-Compat-0.12_1, p5-Mail-Tools-2.14, p5-Module-Implementation-0.09_1, p5-Module-Runtime-0.014_1, p5-Module-Runtime-Conflicts-0.003, p5-Moose-2.1804,1, p5-MooseX-FollowPBP-0.05_1, p5-MooseX-Types-0.46, p5-Net-DNS-1.06_2,1, p5-Net-Domain-TLD-1.74, p5-Package-DeprecationManager-0.15, p5-Package-Stash-0.37_1, p5-Package-Stash-XS-0.28_1, p5-Params-Coerce-0.14_2, p5-Params-Util-1.07_2, p5-Params-Validate-1.24, p5-Parse-RecDescent-1.967.009_2, p5-Scalar-List-Utils-1.45,1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-ForMethods-0.100052, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Identify-0.12, p5-Sub-Install-0.928_1, p5-Sub-Name-0.14,1, p5-Text-CSV_XS-1.18, p5-TimeDate-2.30_2,1, p5-Try-Tiny-0.24, p5-URI-1.71, p5-Variable-Magic-0.59, p5-namespace-autoclean-0.28, p5-namespace-clean-0.27, perl5-5.20.3_15
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-1.06_1, perl5-5.20.3_15
Also listed in: Perl5

p5-Bio-Phylo-0.58
Phylogenetic analysis using Perl
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.6_1,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, graphite2-1.3.8, graphviz-2.38.0_13, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgd-2.2.2,1, libglapi-11.2.2, libiconv-1.14_9, libltdl-2.4.6, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.30, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.12, p5-Authen-NTLM-1.09_1, p5-Class-AutoClass-1.56_1, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.28_1, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-BinHex-1.125, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.035, p5-DBI-1.636, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Data-TemporaryBag-0.09_1, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17024, p5-Exception-Class-1.40, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-Font-TTF-1.05, p5-GD-2.56_3, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.21, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.13, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.03_1, p5-HTTP-Cookies-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-Hash-AutoHash-1.17_1, p5-Hash-AutoHash-Args-1.18_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-SessionData-1.03_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-IO-String-1.08_1, p5-IO-Tty-1.12_1, p5-IO-stringy-2.111, p5-IPC-Run-0.94, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.507,2, p5-Mail-Tools-2.14, p5-Math-Bezier-Convert-0.02_1, p5-Math-CDF-0.1_2, p5-Math-Derivative-0.04, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.014_1, p5-Moo-2.002004, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-OLE-Storage_Lite-0.19_1, p5-PDF-API2-2.028, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000003, p5-SOAP-Lite-1.20, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-SWF-Builder-0.16_2, p5-SWF-File-0.42_2,1, p5-Set-Scalar-1.26_1, p5-Socket-2.021, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Install-0.928_1, p5-Sub-Uplevel-0.2500, p5-Task-Weaken-1.04_1, p5-Test-Deep-1.120, p5-Test-Differences-0.630,1, p5-Test-Exception-0.43, p5-Test-Most-0.34_1, p5-Test-Simple-1.302037, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_3, p5-Text-Shellwords-1.08_1, p5-Text-Tabs+Wrap-2013.0523_1, p5-Tie-IxHash-1.23_1, p5-Tie-ToObject-0.03_2, p5-TimeDate-2.30_2,1, p5-Tree-DAG_Node-1.29, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.71, 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-2.0126,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.721, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.08_1, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.56, p5-XML-Simple-2.22, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XML2JSON-0.06_1, p5-XML-XPath-1.37, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-Syck-1.27_1, p5-bioperl-1.6.924_4, p5-libwww-6.15, p5-libxml-0.08_1, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, printproto-1.0.5, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
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-3.26, curl-7.50.1, io_lib-1.14.8, perl5-5.20.3_15
Also listed in: Perl5

p5-bioperl-1.6.924_4
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.6_1,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, graphite2-1.3.8, graphviz-2.38.0_13, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgd-2.2.2,1, libglapi-11.2.2, libiconv-1.14_9, libltdl-2.4.6, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.30, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.12, p5-Authen-NTLM-1.09_1, p5-CPAN-Meta-2.150005, p5-Class-AutoClass-1.56_1, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.28_1, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Convert-BinHex-1.125, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.035, p5-DBI-1.636, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17024, p5-Exception-Class-1.40, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_3, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.21, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.13, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.03_1, p5-HTTP-Cookies-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-Hash-AutoHash-1.17_1, p5-Hash-AutoHash-Args-1.18_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-SessionData-1.03_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-IO-String-1.08_1, p5-IO-Tty-1.12_1, p5-IO-stringy-2.111, p5-IPC-Run-0.94, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.507,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.04, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Build-0.4218, p5-Module-Runtime-0.014_1, p5-Moo-2.002004, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000003, p5-SOAP-Lite-1.20, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.26_1, p5-Socket-2.021, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Install-0.928_1, p5-Sub-Uplevel-0.2500, p5-Task-Weaken-1.04_1, p5-Test-Deep-1.120, p5-Test-Differences-0.630,1, p5-Test-Exception-0.43, p5-Test-Most-0.34_1, p5-Test-Simple-1.302037, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_3, p5-Text-Shellwords-1.08_1, p5-Text-Tabs+Wrap-2013.0523_1, p5-Tie-IxHash-1.23_1, p5-Tie-ToObject-0.03_2, p5-TimeDate-2.30_2,1, p5-Tree-DAG_Node-1.29, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.71, 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-2.0126,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.721, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.08_1, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.56, p5-XML-Simple-2.22, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.37, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-libwww-6.15, p5-libxml-0.08_1, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, printproto-1.0.5, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
Also listed in: Perl5

p5-bioperl-run-1.6.901_1
Wrapper modules for common bioinformatics tools
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.6_1,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, graphite2-1.3.8, graphviz-2.38.0_13, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libgd-2.2.2,1, libglapi-11.2.2, libiconv-1.14_9, libltdl-2.4.6, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.30, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.12, p5-Authen-NTLM-1.09_1, p5-CPAN-Meta-2.150005, p5-Class-AutoClass-1.56_1, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.28_1, p5-Class-Method-Modifiers-2.12, p5-Clone-0.38, p5-Config-Any-0.27, p5-Config-General-2.63, p5-Config-Tiny-2.23, p5-Convert-BinHex-1.125, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.035, p5-DBI-1.636, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.01, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17024, p5-Exception-Class-1.40, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-File-Sort-1.01_1, p5-GD-2.56_3, p5-GD-SVG-0.33_6, p5-Graph-0.96_2,1, p5-GraphViz-2.21, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.13, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.03_1, p5-HTTP-Cookies-6.01_1, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.11, p5-HTTP-Negotiate-6.01_1, p5-Hash-AutoHash-1.17_1, p5-Hash-AutoHash-Args-1.18_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-SessionData-1.03_1, p5-IO-Socket-IP-0.37_1, p5-IO-Socket-SSL-2.037, p5-IO-String-1.08_1, p5-IO-Tty-1.12_1, p5-IO-stringy-2.111, p5-IPC-Run-0.94, p5-JSON-XS-3.02, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.507,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.04, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, p5-Module-Build-0.4218, p5-Module-Pluggable-5.2, p5-Module-Runtime-0.014_1, p5-Moo-2.002004, p5-Mozilla-CA-20160104, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.77, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000003, p5-SOAP-Lite-1.20, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.26_1, p5-Socket-2.021, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Install-0.928_1, p5-Sub-Uplevel-0.2500, p5-Task-Weaken-1.04_1, p5-Test-Deep-1.120, p5-Test-Differences-0.630,1, p5-Test-Exception-0.43, p5-Test-Most-0.34_1, p5-Test-Simple-1.302037, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_3, p5-Text-Shellwords-1.08_1, p5-Text-Tabs+Wrap-2013.0523_1, p5-Tie-IxHash-1.23_1, p5-Tie-ToObject-0.03_2, p5-TimeDate-2.30_2,1, p5-Tree-DAG_Node-1.29, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.71, 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-2.0126,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.721, p5-XML-RegExp-0.04_1, p5-XML-SAX-0.99_2, p5-XML-SAX-Base-1.08_1, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.56, p5-XML-Simple-2.22, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.37, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-LibYAML-0.59_1, p5-bioperl-1.6.924_4, p5-common-sense-3.74, p5-libwww-6.15, p5-libxml-0.08_1, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, printproto-1.0.5, python27-2.7.12, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
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-2.27_1,1, cd-hit-4.6.4, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4, p5-URI-1.71, perl5-5.20.3_15
Also listed in: Perl5

paml-4.9a
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: jrm@ftfl.ca
Requires: gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4

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-4.3.46_1, gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-3.5.11_4, libXt-1.1.5,1, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, printproto-1.0.5, xextproto-7.3.0, xproto-7.0.28

phyml-3.2.0
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-0.2.4, libtool-2.4.6, m4-1.4.17_1,1, perl5-5.20.3_15, pkgconf-1.0.1

plink-1.07_4
Whole genome association analysis toolset
Long description | Changes | Main Web Site
Maintained by: bacon4000@gmail.com
Requires: binutils-2.27_1,1, blas-3.5.0_3, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, lapack-3.5.0, mpc-1.0.3, mpfr-3.1.4
Also listed in: Science

plinkseq-0.10
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, gmake-4.2.1_1, indexinfo-0.2.4
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, gmake-4.2.1_1, indexinfo-0.2.4

protomol-2.0.3_12
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, dri2proto-2.8, expat-2.2.0, fixesproto-5.0, freeglut-3.0.0, inputproto-2.3.1, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libGL-11.2.2, libGLU-9.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.6,1, libXmu-1.1.2_3,1, libXrandr-1.5.0, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libglapi-11.2.2, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, pciids-20160621, png-1.6.23, randrproto-1.5.0, renderproto-0.11.1, tiff-4.0.6_2, videoproto-2.3.2, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.28

psi88-1.0_8
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

py27-biom-format-2.1.5_1
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@ftfl.ca
Requires: binutils-2.27_1,1, blas-3.5.0_3, cblas-1.0_4, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, hdf-szip-2.1_2, hdf5-1.10.0, indexinfo-0.2.4, lapack-3.5.0, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.4, openblas-0.2.18_1,1, perl5-5.20.3_15, postgresql93-client-9.3.14, py27-click-6.6, py27-future-0.15.2_1, py27-h5py-2.6.0, py27-numpy-1.11.1,1, py27-pyqi-0.3.2, py27-scipy-0.16.1, py27-setuptools27-23.1.0, py27-six-1.10.0, python27-2.7.12, suitesparse-4.0.2_4, swig13-1.3.40_1
Also listed in: Python

py27-biopython-1.66
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: binutils-2.27_1,1, blas-3.5.0_3, cblas-1.0_4, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, lapack-3.5.0, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.4, openblas-0.2.18_1,1, py27-numpy-1.11.1,1, py27-reportlab1-1.21.2_3, py27-setuptools27-23.1.0, python2-2_3, python27-2.7.12, suitesparse-4.0.2_4
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-2.27_1,1, blas-3.5.0_3, cblas-1.0_4, cython-0.24, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, lapack-3.5.0, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.4, openblas-0.2.18_1,1, py27-Babel-2.3.4, py27-Jinja2-2.8, py27-MarkupSafe-0.23, py27-alabaster-0.7.6, py27-docutils-0.12, py27-imagesize-0.7.1, py27-numpy-1.11.1,1, py27-pygments-2.1.3, py27-pystemmer-1.3.0_1, py27-pytz-2016.6.1,1, py27-setuptools27-23.1.0, py27-six-1.10.0, py27-snowballstemmer-1.2.0_1, py27-sphinx-1.4.4, py27-sphinx_rtd_theme-0.1.9, py27-sqlalchemy10-1.0.14, py27-sqlite3-2.7.12_7, python27-2.7.12, sqlite3-3.14.1, suitesparse-4.0.2_4
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-2.27_1,1, blas-3.5.0_3, cblas-1.0_4, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, lapack-3.5.0, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.4, openblas-0.2.18_1,1, py27-numpy-1.11.1,1, py27-setuptools27-23.1.0, python27-2.7.12, suitesparse-4.0.2_4
Also listed in: Python

python-nexus-1.35
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, indexinfo-0.2.4, libffi-3.2.1, py27-setuptools27-23.1.0, python27-2.7.12
Also listed in: Python

raster3d-3.0.2_7
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ImageMagick-6.9.5.7,1, avahi-app-0.6.31_5, binutils-2.27_1,1, ca_root_nss-3.26, cairo-1.14.6_1,2, cups-2.1.4, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, fftw3-3.3.3_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, freetype2-2.6.3, gbm-11.2.2, gcc-4.8.5_2, gcc-ecj-4.5, gdbm-1.12, gdk-pixbuf2-2.32.3_1, gettext-runtime-0.19.8.1, ghostscript9-agpl-base-9.16_5, ghostscript9-agpl-x11-9.16_2, giflib-5.1.3, glib-2.46.2_2, glproto-1.4.17, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gsfonts-8.11_6, harfbuzz-1.3.0, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, jasper-1.900.1_16, jbig2dec-0.13, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, lcms2-2.7_2, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXi-1.7.6,1, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libcroco-0.6.11, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libfpx-1.3.1.4_1, libgd-2.2.2,1, libglapi-11.2.2, libgsf-1.14.36, libiconv-1.14_9, libidn-1.33_1, liblqr-1-0.4.1_8, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.13.4, libpthread-stubs-0.3_6, librsvg2-2.40.16, libtasn1-4.9, libwmf-0.2.8.4_15, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpfr-3.1.4, nettle-3.2, openjpeg-2.1.1, p11-kit-0.23.2, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, pkgconf-1.0.1, png-1.6.23, python2-2_3, python27-2.7.12, renderproto-0.11.1, svgalib-1.4.3_7, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, webp-0.5.0, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.28
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

ruby22-bio-1.5.0
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: indexinfo-0.2.4, libedit-3.1.20150325_2,1, libffi-3.2.1, libyaml-0.1.6_2, ruby-2.2.5,1
Also listed in: Ruby

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-3.26, curl-7.50.1, gettext-runtime-0.19.8.1, gmake-4.2.1_1, htslib-1.3.1, indexinfo-0.2.4, m4-1.4.17_1,1, perl5-5.20.3_15

seaview-4.6
Multiple DNA/protein sequence alignment editor
Long description | Changes | Main Web Site
Maintained by: bofh@FreeBSD.org
Requires: damageproto-1.2.1, dri2proto-2.8, expat-2.2.0, fixesproto-5.0, fltk-1.3.3_2, fontconfig-2.12.1,1, freetype2-2.6.3, gettext-runtime-0.19.8.1, gmake-4.2.1_1, indexinfo-0.2.4, jpeg-turbo-1.4.2, kbproto-1.0.7, libGL-11.2.2, libGLU-9.0.0_2, libX11-1.6.3,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXinerama-1.1.3_3,1, libXrender-0.9.9, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libglapi-11.2.2, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, pciids-20160621, png-1.6.23, renderproto-0.11.1, videoproto-2.3.2, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.28

seqan-2.1.1_1
C++ Sequence Analysis Template Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqan-apps-2.1.1
Official Bioinformatic applications based on the SeqAn library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: binutils-2.27_1,1, boost-libs-1.55.0_12, ca_root_nss-3.26, cmake-3.6.1, cmake-modules-3.6.1, curl-7.50.1, expat-2.2.0, gcc-ecj-4.5, gcc49-4.9.4, gettext-runtime-0.19.8.1, gmp-5.1.3_3, icu-55.1,1, indexinfo-0.2.4, jsoncpp-1.7.3, libarchive-3.2.1,1, liblz4-131, lzo2-2.09, mpc-1.0.3, mpfr-3.1.4

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-4.43.0
Tools for visualising sequence alignments
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: atk-2.18.0, avahi-app-0.6.31_5, ca_root_nss-3.26, cairo-1.14.6_1,2, clang36-3.6.2, compositeproto-0.4.2, cups-2.1.4, curl-7.50.1, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gdbm-1.12, gdk-pixbuf2-2.32.3_1, gettext-runtime-0.19.8.1, gettext-tools-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gtk-update-icon-cache-2.24.29, gtk2-2.24.29_2, harfbuzz-1.3.0, hicolor-icon-theme-0.15, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, jasper-1.900.1_16, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXi-1.7.6,1, libXinerama-1.1.3_3,1, libXrandr-1.5.0, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libglapi-11.2.2, libiconv-1.14_9, libidn-1.33_1, libpaper-1.1.24.4, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libtasn1-4.9, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm36-3.6.2_2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.2, p11-kit-0.23.2, pango-1.38.0_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, pkgconf-1.0.1, png-1.6.23, python-2.7_2,2, python2-2_3, python27-2.7.12, randrproto-1.5.0, renderproto-0.11.1, shared-mime-info-1.5, sqlite3-3.14.1, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, xcb-util-0.4.0_1,1, 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-7.0.28

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_2
Very fast matching and alignment of DNA sequences
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmake-4.2.1_1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

tRNAscan-SE-1.23_1
Improved tool for transfer RNA detection
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.20.3_15

t_coffee-9.03_3
Multiple DNA or protein sequence alignment package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.27_1,1, clustalw-2.1_1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

tinker-7.1.3
General purpose molecular modelling package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.27_1,1, gcc-4.8.5_2, gcc-ecj-4.5, gettext-runtime-0.19.8.1, gmp-5.1.3_3, indexinfo-0.2.4, mpc-1.0.3, mpfr-3.1.4

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

treeviewx-0.5.1s20100823_2
Phylogenetic tree viewer
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_1, atk-2.18.0, avahi-app-0.6.31_5, ca_root_nss-3.26, cairo-1.14.6_1,2, compositeproto-0.4.2, cups-2.1.4, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dconf-0.24.0_1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.2.0, 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, freetype2-2.6.3, gbm-11.2.2, gconf2-3.2.6_4, gdbm-1.12, gdk-pixbuf2-2.32.3_1, gettext-runtime-0.19.8.1, glib-2.46.2_2, glproto-1.4.17, gmake-4.2.1_1, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gstreamer-0.10.36_4, gstreamer-plugins-0.10.36_6,3, gtk-update-icon-cache-2.24.29, gtk2-2.24.29_2, harfbuzz-1.3.0, hicolor-icon-theme-0.15, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, jasper-1.900.1_16, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, libEGL-11.2.2, libGL-11.2.2, libGLU-9.0.0_2, libICE-1.0.9_1,1, libIDL-0.8.14_2, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.14_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXft-2.3.2_1, libXi-1.7.6,1, libXinerama-1.1.3_3,1, libXrandr-1.5.0, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libfontenc-1.1.3, libglapi-11.2.2, libiconv-1.14_9, libidn-1.33_1, libmspack-0.5, libpaper-1.1.24.4, libpciaccess-0.13.4, libpthread-stubs-0.3_6, libtasn1-4.9, libxcb-1.11.1, libxml2-2.9.3, libxshmfence-1.2, llvm37-3.7.1_3, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-3.2, nspr-4.12, orc-0.4.25, p11-kit-0.23.2, pango-1.38.0_1, pangox-compat-0.0.2_1, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, polkit-0.113_1, python-2.7_2,2, python2-2_3, python27-2.7.12, randrproto-1.5.0, renderproto-0.11.1, shared-mime-info-1.5, spidermonkey170-17.0.0_1, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, wx28-gtk2-2.8.12_6, wx28-gtk2-common-2.8.12_6, wx28-gtk2-contrib-2.8.12_6, wx28-gtk2-contrib-common-2.8.12_6, xcb-util-0.4.0_1,1, 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-7.0.28

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-2.35, expat-2.2.0, fixesproto-5.0, fontconfig-2.12.1,1, freetype2-2.6.3, giflib-5.1.3, inputproto-2.3.1, java-zoneinfo-2016.f, javavmwrapper-2.5_2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.6,1, libXrender-0.9.9, libXt-1.1.5,1, libXtst-1.2.2_3, libfontenc-1.1.3, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk8-8.102.14, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.28
Also listed in: Java

ugene-1.22.0_1
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-4.3.46_1, ca_root_nss-3.26, cairo-1.14.6_1,2, compositeproto-0.4.2, cups-2.1.4, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, desktop-file-utils-0.22_3, dri2proto-2.8, expat-2.2.0, fixesproto-5.0, fontcacheproto-0.1.3, fontconfig-2.12.1,1, freetype2-2.6.3, gbm-11.2.2, gdbm-1.12, gettext-runtime-0.19.8.1, giflib-5.1.3, glib-2.46.2_2, glproto-1.4.17, gmp-5.1.3_3, gnome_subr-1.0, gnutls-3.4.14, gobject-introspection-1.46.0, graphite2-1.3.8, gstreamer1-1.8.0, gstreamer1-plugins-1.8.0, harfbuzz-1.3.0, hicolor-icon-theme-0.15, icu-55.1,1, indexinfo-0.2.4, inputproto-2.3.1, iso-codes-3.69, jasper-1.900.1_16, jbigkit-2.1_1, jpeg-turbo-1.4.2, kbproto-1.0.7, lcms-1.19_6,1, libEGL-11.2.2, libGL-11.2.2, libGLU-9.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, 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-5.0.1_3, libXfontcache-1.0.5_3, libXi-1.7.6,1, libXmu-1.1.2_3,1, libXrender-0.9.9, libXt-1.1.5,1, libXv-1.0.10_3,1, libXvMC-1.0.9, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.66,1, libedit-3.1.20150325_2,1, libffi-3.2.1, libgcrypt-1.7.3, libglapi-11.2.2, libgpg-error-1.24, libiconv-1.14_9, libidn-1.33_1, libmng-1.0.10_2, libpaper-1.1.24.4, libpciaccess-0.13.4, libproxy-0.4.12, libpthread-stubs-0.3_6, libtasn1-4.9, libxcb-1.11.1, libxkbcommon-0.5.0_1, libxml2-2.9.3, libxshmfence-1.2, libxslt-1.1.29, llvm37-3.7.1_3, nettle-3.2, orc-0.4.25, p11-kit-0.23.2, pciids-20160621, pcre-8.39, perl5-5.20.3_15, pixman-0.34.0, png-1.6.23, python2-2_3, python27-2.7.12, qt5-buildtools-5.5.1, qt5-core-5.5.1_2, qt5-dbus-5.5.1, qt5-gui-5.5.1_1, qt5-imageformats-5.5.1_1, qt5-linguisttools-5.5.1, qt5-network-5.5.1, qt5-opengl-5.5.1, qt5-printsupport-5.5.1_1, qt5-qmake-5.5.1_1, qt5-qml-5.5.1, qt5-quick-5.5.1, qt5-script-5.5.1, qt5-scripttools-5.5.1, qt5-sql-5.5.1, qt5-svg-5.5.1, qt5-testlib-5.5.1, qt5-webkit-5.5.1_3, qt5-widgets-5.5.1_1, qt5-xml-5.5.1, qt5-xmlpatterns-5.5.1, renderproto-0.11.1, sqlite3-3.14.1, tiff-4.0.6_2, tpm-emulator-0.7.4_1, trousers-0.3.13, videoproto-2.3.2, webp-0.5.0, xcb-util-0.4.0_1,1, 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, xprop-1.2.2, xproto-7.0.28, xset-1.2.3_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, gmake-4.2.1_1, indexinfo-0.2.4, m4-1.4.17_1,1, perl5-5.20.3_15, pkgconf-1.0.1

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, gmake-4.2.1_1, indexinfo-0.2.4, libffi-3.2.1, perl5-5.20.3_15, python27-2.7.12

wise-2.4.1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1, glib-2.46.2_2, indexinfo-0.2.4, libffi-3.2.1, libiconv-1.14_9, pcre-8.39, perl5-5.20.3_15, pkgconf-1.0.1, python27-2.7.12

xmolwt-0.7_6
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, glib12-1.2.10_15, gmake-4.2.1_1, gtk12-1.2.10_24, indexinfo-0.2.4, inputproto-2.3.1, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.6,1, libpthread-stubs-0.3_6, libxcb-1.11.1, libxml2-2.9.3, xextproto-7.3.0, xproto-7.0.28

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