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FreeBSD Ports: Biology

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Biologie-Software.

InsightToolkit-4.7.2
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@gmail.com
Requires: ca_root_nss-3.20, cmake-3.2.3_2, cmake-modules-3.2.3, curl-7.44.0, expat-2.1.0_3, jsoncpp-0.6.0.r2_2, libarchive-3.1.2_4,1, lzo2-2.09
Also listed in: Science

afni-2012.04.17.2129_12
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: R-3.0.2_7, binutils-2.25.1, ca_root_nss-3.20, cairo-1.14.2,2, cups-client-2.0.3_2, cups-image-2.0.3_2, curl-7.44.0, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, endian-1.1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gettext-tools-0.19.5.1, ghostscript9-base-9.06_11, glib-2.44.1_1, glproto-1.4.17, gmake-4.1_2, gmp-5.1.3_2, gnutls-3.3.17.1, graphite2-1.3.0, gsed-4.2.2, gsfonts-8.11_6, gsl-1.16_2, harfbuzz-1.0.1, hdf-szip-2.1_2, hdf5-1.8.15_1, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, jasper-1.900.1_15, jbig2dec-0.11_4, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, lcms2-2.7_1, libEGL-10.4.6, libGL-10.4.6, libGLU-9.0.0_2, libGLw-8.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-1.7.4_1,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.11_4, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libgcrypt-1.6.3, libglapi-10.4.6, libgpg-error-1.19_1, libiconv-1.14_8, libidn-1.31, libpaper-1.1.24.4, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libtasn1-4.5_1, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mDNSResponder-567, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpeg_encode-1.5b, mpfr-3.1.2_2, netcdf-4.3.3.1_1, netcdf-fortran-4.4.2, netpbm-10.35.96, nettle-2.7.1, open-motif-2.3.4_2, p11-kit-0.23.1_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, qhull5-1.0_3, renderproto-0.11.1, scrnsaverproto-1.2.2, svgalib-1.4.3_7, tcl86-8.6.4, tiff-4.0.4, tk86-8.6.4, trousers-tddl-0.3.10_7, whirlgif-3.04, 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-7.0.27
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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3

artemis-9_1
DNA sequence viewer and annotation tool
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.0.29, dejavu-2.35, expat-2.1.0_3, fixesproto-5.0, fontconfig-2.11.1,1, freetype2-2.6_1, inputproto-2.3.1, java-zoneinfo-2015.f, javavmwrapper-2.5, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.4_1,1, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXtst-1.2.2_3, libfontenc-1.1.2_3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk-7.80.15_1,1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.27
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-3.20, cmake-3.2.3_2, cmake-modules-3.2.3, curl-7.44.0, expat-2.1.0_3, jsoncpp-0.6.0.r2_2, libarchive-3.1.2_4,1, 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-1.2
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, gsl-1.16_2, htslib-1.2.1, indexinfo-0.2.3

biococoa-2.2.2_1
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: theraven@FreeBSD.org
Requires: avahi-app-0.6.31_5, ca_root_nss-3.20, cairo-1.14.2,2, cups-client-2.0.3_2, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dri2proto-2.8, expat-2.1.0_3, fixesproto-5.0, flac-1.3.1, fontconfig-2.11.1,1, freetype2-2.6_1, gdbm-1.11_2, gettext-runtime-0.19.5.1, giflib-5.0.6, glib-2.44.1_1, glproto-1.4.17, gmake-4.1_2, gmp-5.1.3_2, gnome_subr-1.0, gnustep-back-0.24.1, gnustep-base-1.24.8, gnustep-gui-0.24.1, gnustep-make-2.6.7, gnutls-3.3.17.1, gobject-introspection-1.44.0, icu-55.1, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libGLU-9.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libao-1.2.0_1, libdaemon-0.14_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libgcrypt-1.6.3, libglapi-10.4.6, libgpg-error-1.19_1, libiconv-1.14_8, libidn-1.31, libobjc2-1.8.1, libogg-1.3.2_1,4, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libsndfile-1.0.25_5, libtasn1-4.5_1, libvorbis-1.3.5,3, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, libxslt-1.1.28_7, mDNSResponder-567, nettle-2.7.1, p11-kit-0.23.1_1, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, python2-2_3, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, trousers-tddl-0.3.10_7, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.27
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-1.0.29, apache-ant-1.9.4, dejavu-2.35, expat-2.1.0_3, fixesproto-5.0, fontconfig-2.11.1,1, freetype2-2.6_1, inputproto-2.3.1, java-zoneinfo-2015.f, javavmwrapper-2.5, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.4_1,1, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXtst-1.2.2_3, libfontenc-1.1.2_3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk-7.80.15_1,1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.27
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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, libedit-3.1.20150325_1, mysql56-client-5.6.26, png-1.6.17_1

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-0.19.5.1, indexinfo-0.2.3, 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_3, linux_base-c6-6.6_6, perl5-5.20.2_6, 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-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmake-4.1_2, gmp-5.1.3_2, indexinfo-0.2.3, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.2_2, python27-2.7.10
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-2.16.0, ca_root_nss-3.20, cairo-1.14.2,2, cantarell-fonts-0.0.16, compositeproto-0.4.2, cups-client-2.0.3_2, curl-7.44.0, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dconf-0.24.0, dejavu-2.35, dri2proto-2.8, enchant-1.6.0_5, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gconf2-3.2.6_4, gdk-pixbuf2-2.31.6, geoclue-2.1.10, gettext-runtime-0.19.5.1, giflib-5.0.6, glib-2.44.1_1, glib-networking-2.44.0, glproto-1.4.17, gmp-5.1.3_2, gnome_subr-1.0, gnutls-3.3.17.1, gobject-introspection-1.44.0, graphite2-1.3.0, gsettings-desktop-schemas-3.16.1, gstreamer-0.10.36_4, gstreamer-plugins-0.10.36_6,3, gstreamer1-1.4.5_1, gstreamer1-plugins-1.4.5_2, gtk-update-icon-cache-2.24.28, gtk2-2.24.28_1, harfbuzz-1.0.1, hicolor-icon-theme-0.15, hunspell-1.3.3, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, iso-codes-3.60, jasper-1.900.1_15, jbigkit-2.1_1, jpeg-8_6, json-glib-1.0.4, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libGLU-9.0.0_2, libICE-1.0.9_1,1, libIDL-0.8.14_2, libSM-1.2.2_3,1, libX11-1.6.2_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-1.7.4_1,1, libXinerama-1.1.3_3,1, libXrandr-1.4.2_3, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXv-1.0.10_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libgcrypt-1.6.3, libglapi-10.4.6, libgpg-error-1.19_1, libiconv-1.14_8, libidn-1.31, libmspack-0.5, libpciaccess-0.13.3, libproxy-0.4.6, libpthread-stubs-0.3_6, libsecret-0.18.3, libsoup-2.50.0, libtasn1-4.5_1, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, libxslt-1.1.28_7, mDNSResponder-567, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-2.7.1, nspr-4.10.9, orc-0.4.24_1, p11-kit-0.23.1_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, polkit-0.113, py27-setuptools27-17.0, py27-wxPython-common-3.0.2.0_1, py27-wxPython30-3.0.2.0, python-2.7_2,2, python2-2_3, python27-2.7.10, randrproto-1.4.1, renderproto-0.11.1, shared-mime-info-1.4, spidermonkey170-17.0.0_1, sqlite3-3.8.11.1, tiff-4.0.4, trousers-tddl-0.3.10_7, videoproto-2.3.2, webkit-gtk2-2.4.9, webp-0.4.3, wx30-gtk2-3.0.2_3, 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-7.0.27
Also listed in: Deskutils, Python

emboss-6.6.0_2
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-2.1.0_3, fontconfig-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libgd-2.1.0_6,1, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, open-motif-2.3.4_2, png-1.6.17_1, primer3-2.3.6, printproto-1.0.5, renderproto-0.11.1, tiff-4.0.4, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.27

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

fasta3-36.3.7a
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

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

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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, kbproto-1.0.6, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, xproto-7.0.27

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-4.3.42, gawk-4.1.3_2, gettext-runtime-0.19.5.1, indexinfo-0.2.3, libsigsegv-2.10_1

gmap-2006.04.21_1
Genomic Mapping and Alignment Program for mRNA and EST Sequences
Long description | Changes | Main Web Site
Maintained by: rpz@cse.wustl.edu
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, perl5-5.20.2_6

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-2.16.0, ca_root_nss-3.20, cairo-1.14.2,2, compositeproto-0.4.2, cups-client-2.0.3_2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gdk-pixbuf2-2.31.6, gettext-runtime-0.19.5.1, gettext-tools-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, gmp-5.1.3_2, gnutls-3.3.17.1, graphite2-1.3.0, gtk-update-icon-cache-2.24.28, gtk2-2.24.28_1, harfbuzz-1.0.1, hicolor-icon-theme-0.15, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, jasper-1.900.1_15, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_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-1.7.4_1,1, libXinerama-1.1.3_3,1, libXrandr-1.4.2_3, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libgcrypt-1.6.3, libglapi-10.4.6, libgpg-error-1.19_1, libiconv-1.14_8, libidn-1.31, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libtasn1-4.5_1, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mDNSResponder-567, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-2.7.1, p11-kit-0.23.1_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, pkgconf-0.9.12, png-1.6.17_1, python-2.7_2,2, python2-2_3, python27-2.7.10, randrproto-1.4.1, renderproto-0.11.1, shared-mime-info-1.4, tiff-4.0.4, trousers-tddl-0.3.10_7, 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-7.0.27

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3

hmmer-3.0_1
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: perl5-5.20.2_6

htslib-1.2.1
C library for high-throughput sequencing data formats
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69, autoconf-wrapper-20131203, gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, m4-1.4.17_1,1, perl5-5.20.2_6
Also listed in: Devel

io_lib-1.14.0
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: ca_root_nss-3.20, curl-7.44.0, gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3

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-1.0.29, apache-ant-1.9.4, dejavu-2.35, expat-2.1.0_3, fixesproto-5.0, fontconfig-2.11.1,1, freetype2-2.6_1, inputproto-2.3.1, java-zoneinfo-2015.f, javavmwrapper-2.5, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.4_1,1, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXtst-1.2.2_3, libfontenc-1.1.2_3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, mkfontdir-1.0.7, mkfontscale-1.1.2, openjdk-7.80.15_1,1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.27
Also listed in: Java

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: perl5-5.20.2_6

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

libsbml-5.11.4_1
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.20, cmake-3.2.3_2, cmake-modules-3.2.3, curl-7.44.0, expat-2.1.0_3, jsoncpp-0.6.0.r2_2, libarchive-3.1.2_4,1, libxml2-2.9.2_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-c6-6.6_6

mafft-7.221
Multiple alignment program for amino acid or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3

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_3
Medical Imaging NetCDF
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69, autoconf-wrapper-20131203, automake-1.15, automake-wrapper-20131203, bash-4.3.42, bison-2.7.1,1, ca_root_nss-3.20, curl-7.44.0, gettext-runtime-0.19.5.1, gmake-4.1_2, hdf-szip-2.1_2, hdf5-1.8.15_1, indexinfo-0.2.3, libtool-2.4.6, m4-1.4.17_1,1, netcdf-4.3.3.1_1, perl5-5.20.2_6
Also listed in: Science

molden-5.0.7_2
Display molecular orbitals and electron densities in 2D and 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.25.1, damageproto-1.2.1, dri2proto-2.8, expat-2.1.0_3, fixesproto-5.0, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, glproto-1.4.17, gmake-4.1_2, gmp-5.1.3_2, indexinfo-0.2.3, kbproto-1.0.6, libGL-10.4.6, libGLU-9.0.0_2, libX11-1.6.2_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, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libglapi-10.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mpc-1.0.3, mpfr-3.1.2_2, pciids-20150731, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.27

mopac-7.1.15
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmake-4.1_2, gmp-5.1.3_2, indexinfo-0.2.3, mpc-1.0.3, mpfr-3.1.2_2

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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, 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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, perl5-5.20.2_6

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: jwbacon@tds.net
Requires: binutils-2.25.1, bzip2-1.0.6, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmake-4.1_2, gmp-5.1.3_2, indexinfo-0.2.3, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.2_2, p5-Exporter-Tiny-0.042_1, p5-List-MoreUtils-0.413, pcre-8.37_4, perl5-5.20.2_6, python27-2.7.10

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-2.1.0_3, fontconfig-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, indexinfo-0.2.3, jpeg-8_6, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, open-motif-2.3.4_2, png-1.6.17_1, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.27

njplot-2.1_3
Phylogenetic tree drawing program capable of interactive manipulation
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: expat-2.1.0_3, fontconfig-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, indexinfo-0.2.3, jpeg-8_6, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, ncbi-toolkit-2012.06.20, open-motif-2.3.4_2, png-1.6.17_1, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.27

ortep3-1.0.3_9
Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, mpc-1.0.3, mpfr-3.1.2_2

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, perl5-5.20.2_6
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-1.14.2,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, graphite2-1.3.0, graphviz-2.38.0_8, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libedit-3.1.20150325_1, libffi-3.2.1, libfontenc-1.1.2_3, libgd-2.1.0_6,1, libglapi-10.4.6, libiconv-1.14_8, libltdl-2.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.26, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.11_1, 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-2.11_1, p5-Clone-0.38, p5-Convert-BinHex-1.124, p5-Convert-Binary-C-0.77, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.032, p5-DBI-1.634, p5-Data-OptList-0.109_1, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.00, 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-1.39, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_2, p5-GD-SVG-0.33_6, p5-Graph-0.96_1,1, p5-GraphViz-2.18, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.71_1, 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-6.10, 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, p5-IO-Socket-SSL-2.016, 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-5.506,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.03, p5-Math-Random-0.71_2, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.014_1, p5-Moo-2.000002, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_1, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000001, p5-SOAP-Lite-1.14, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.42,1, p5-Set-Scalar-1.26_1, p5-Socket-2.020, 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-0.117_1, p5-Test-Differences-0.630,1, p5-Test-Exception-0.40, p5-Test-Most-0.34_1, p5-Test-NoWarnings-1.04_2, p5-Test-Simple-1.001.014, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_2, 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-1.27, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.69, 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-2.0121,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.72, 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-2.20_1, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.13_1, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-bioperl-1.6.924_4, p5-libwww-6.13, p5-libxml-0.08_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, 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-7.0.27
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-1.14.2,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, graphite2-1.3.0, graphviz-2.38.0_8, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libedit-3.1.20150325_1, libffi-3.2.1, libfontenc-1.1.2_3, libgd-2.1.0_6,1, libglapi-10.4.6, libiconv-1.14_8, libltdl-2.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.26, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.11_1, 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-2.11_1, p5-Clone-0.38, p5-Convert-BinHex-1.124, p5-Convert-Binary-C-0.77, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.032, p5-DBI-1.634, p5-Data-OptList-0.109_1, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.00, 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-1.39, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_2, p5-GD-SVG-0.33_6, p5-Graph-0.96_1,1, p5-GraphViz-2.18, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.71_1, 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-6.10, 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, p5-IO-Socket-SSL-2.016, 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-5.506,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.03, p5-Math-Random-0.71_2, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.014_1, p5-Moo-2.000002, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_1, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000001, p5-SOAP-Lite-1.14, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.42,1, p5-Set-Scalar-1.26_1, p5-Socket-2.020, 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-0.117_1, p5-Test-Differences-0.630,1, p5-Test-Exception-0.40, p5-Test-Most-0.34_1, p5-Test-NoWarnings-1.04_2, p5-Test-Simple-1.001.014, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_2, 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-1.27, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.69, 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-2.0121,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.72, 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-2.20_1, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.13_1, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-bioperl-1.6.924_4, p5-libwww-6.13, p5-libxml-0.08_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, 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-7.0.27
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-3.20, curl-7.44.0, 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-3.71_1, 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-6.10, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-IP-0.37, p5-IO-Socket-SSL-2.016, p5-LWP-MediaTypes-6.02_1, p5-Module-Build-0.4214, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-Readonly-2.00_1, p5-Socket-2.020, p5-URI-1.69, p5-WWW-Curl-4.17_2, p5-WWW-RobotRules-6.02_1, p5-libwww-6.13, perl5-5.20.2_6
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-1.69, perl5-5.20.2_6
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-3.71_1, 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-6.10, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-IP-0.37, p5-IO-Socket-SSL-2.016, p5-LWP-MediaTypes-6.02_1, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-Socket-2.020, p5-URI-1.69, p5-WWW-RobotRules-6.02_1, p5-libwww-6.13, perl5-5.20.2_6
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-3.20, cairo-1.14.2,2, curl-7.44.0, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, graphite2-1.3.0, graphviz-2.38.0_8, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, io_lib-1.14.0, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libedit-3.1.20150325_1, libffi-3.2.1, libfontenc-1.1.2_3, libgd-2.1.0_6,1, libglapi-10.4.6, libiconv-1.14_8, libltdl-2.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.26, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.11_1, 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-2.11_1, p5-Clone-0.38, p5-Convert-BinHex-1.124, p5-Convert-Binary-C-0.77, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.032, p5-DBI-1.634, p5-Data-OptList-0.109_1, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.00, 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-1.39, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_2, p5-GD-SVG-0.33_6, p5-Graph-0.96_1,1, p5-GraphViz-2.18, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.71_1, 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-6.10, 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, p5-IO-Socket-SSL-2.016, 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-5.506,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.03, p5-Math-Random-0.71_2, p5-Math-Spline-0.02_1, p5-Module-Build-0.4214, p5-Module-Runtime-0.014_1, p5-Moo-2.000002, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_1, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000001, p5-SOAP-Lite-1.14, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.42,1, p5-Set-Scalar-1.26_1, p5-Socket-2.020, 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-0.117_1, p5-Test-Differences-0.630,1, p5-Test-Exception-0.40, p5-Test-Most-0.34_1, p5-Test-NoWarnings-1.04_2, p5-Test-Simple-1.001.014, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_2, 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-1.27, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.69, 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-2.0121,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.72, 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-2.20_1, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.13_1, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-bioperl-1.6.924_4, p5-libwww-6.13, p5-libxml-0.08_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, 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-7.0.27
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-0.15, p5-Carp-Clan-6.04_1, p5-Class-C3-0.28, p5-Class-Load-0.22, p5-Class-Load-XS-0.09_1, p5-Class-Singleton-1.5_1, p5-Data-OptList-0.109_1, p5-Date-Manip-6.50, p5-DateTime-1.20, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-0.46, p5-DateTime-TimeZone-1.93, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-OverloadInfo-0.004, p5-Devel-StackTrace-2.00, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Email-Valid-1.192_1, p5-Eval-Closure-0.13, p5-Exporter-Tiny-0.042_1, p5-IO-Socket-INET6-2.72_1, p5-List-AllUtils-0.09_1, p5-List-MoreUtils-0.413, p5-MIME-Base32-1.02a_1, 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-0.002, p5-Moose-2.1603,1, p5-MooseX-FollowPBP-0.05_1, p5-MooseX-Types-0.46, p5-Net-DNS-1.01, p5-Net-Domain-TLD-1.73, p5-Package-DeprecationManager-0.14, p5-Package-Stash-0.37_1, p5-Package-Stash-XS-0.28_1, p5-Params-Coerce-0.14_2, p5-Params-Util-1.07_1, p5-Params-Validate-1.21, p5-Parse-RecDescent-1.967.009_2, p5-Socket6-0.25_2, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-ForMethods-0.100052, p5-Sub-Exporter-Progressive-0.001011, p5-Sub-Identify-0.10, p5-Sub-Install-0.928_1, p5-Sub-Name-0.14,1, p5-Task-Weaken-1.04_1, p5-Text-CSV_XS-1.18, p5-TimeDate-2.30_2,1, p5-Try-Tiny-0.22, p5-URI-1.69, p5-Variable-Magic-0.58, p5-namespace-autoclean-0.26, p5-namespace-clean-0.25_2, perl5-5.20.2_6
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, perl5-5.20.2_6
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-1.14.2,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, graphite2-1.3.0, graphviz-2.38.0_8, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libedit-3.1.20150325_1, libffi-3.2.1, libfontenc-1.1.2_3, libgd-2.1.0_6,1, libglapi-10.4.6, libiconv-1.14_8, libltdl-2.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.26, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.11_1, 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-2.11_1, p5-Clone-0.38, p5-Convert-BinHex-1.124, p5-Convert-Binary-C-0.77, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.032, p5-DBI-1.634, p5-Data-OptList-0.109_1, p5-Data-Stag-0.14_2, p5-Data-TemporaryBag-0.09_1, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.00, 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-1.39, 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_2, p5-GD-SVG-0.33_6, p5-Graph-0.96_1,1, p5-GraphViz-2.18, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.71_1, 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-6.10, 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, p5-IO-Socket-SSL-2.016, 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-5.506,2, p5-Mail-Tools-2.14, p5-Math-Bezier-Convert-0.02_1, p5-Math-CDF-0.1_2, p5-Math-Derivative-0.03, p5-Math-Random-0.71_2, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.014_1, p5-Moo-2.000002, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-OLE-Storage_Lite-0.19_1, p5-PDF-API2-2.023, p5-Params-Util-1.07_1, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000001, p5-SOAP-Lite-1.14, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-SWF-Builder-0.16_2, p5-SWF-File-0.42_2,1, p5-Scalar-List-Utils-1.42,1, p5-Set-Scalar-1.26_1, p5-Socket-2.020, 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-0.117_1, p5-Test-Differences-0.630,1, p5-Test-Exception-0.40, p5-Test-Most-0.34_1, p5-Test-NoWarnings-1.04_2, p5-Test-Simple-1.001.014, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_2, 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-1.27, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.69, 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-2.0121,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.72, 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-2.20_1, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XML2JSON-0.06_1, p5-XML-XPath-1.13_1, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-YAML-Syck-1.27_1, p5-bioperl-1.6.924_4, p5-libwww-6.13, p5-libxml-0.08_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, 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-7.0.27
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-3.20, curl-7.44.0, io_lib-1.14.0, perl5-5.20.2_6
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-1.14.2,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, graphite2-1.3.0, graphviz-2.38.0_8, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libedit-3.1.20150325_1, libffi-3.2.1, libfontenc-1.1.2_3, libgd-2.1.0_6,1, libglapi-10.4.6, libiconv-1.14_8, libltdl-2.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.26, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.11_1, 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-2.11_1, p5-Clone-0.38, p5-Convert-BinHex-1.124, p5-Convert-Binary-C-0.77, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.032, p5-DBI-1.634, p5-Data-OptList-0.109_1, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.00, 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-1.39, p5-Exporter-Tiny-0.042_1, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.56_2, p5-GD-SVG-0.33_6, p5-Graph-0.96_1,1, p5-GraphViz-2.18, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.71_1, 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-6.10, 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, p5-IO-Socket-SSL-2.016, 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-5.506,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.03, p5-Math-Random-0.71_2, p5-Math-Spline-0.02_1, p5-Module-Build-0.4214, p5-Module-Runtime-0.014_1, p5-Moo-2.000002, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_1, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000001, p5-SOAP-Lite-1.14, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.42,1, p5-Set-Scalar-1.26_1, p5-Socket-2.020, 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-0.117_1, p5-Test-Differences-0.630,1, p5-Test-Exception-0.40, p5-Test-Most-0.34_1, p5-Test-NoWarnings-1.04_2, p5-Test-Simple-1.001.014, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_2, 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-1.27, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-URI-1.69, 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-2.0121,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.72, 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-2.20_1, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.13_1, p5-XML-XPathEngine-0.14_1, p5-YAML-1.14, p5-libwww-6.13, p5-libxml-0.08_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, 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-7.0.27
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-1.14.2,2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, graphite2-1.3.0, graphviz-2.38.0_8, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libedit-3.1.20150325_1, libffi-3.2.1, libfontenc-1.1.2_3, libgd-2.1.0_6,1, libglapi-10.4.6, libiconv-1.14_8, libltdl-2.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, mysql56-client-5.6.26, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-2.11_1, 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-2.11_1, p5-Clone-0.38, p5-Config-Any-0.26, p5-Config-General-2.58, p5-Config-Tiny-2.22, p5-Convert-BinHex-1.124, p5-Convert-Binary-C-0.77, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.032, p5-DBI-1.634, p5-Data-OptList-0.109_1, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.13_1, p5-Devel-StackTrace-2.00, 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-1.39, 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_2, p5-GD-SVG-0.33_6, p5-Graph-0.96_1,1, p5-GraphViz-2.18, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.71_1, 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-6.10, 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, p5-IO-Socket-SSL-2.016, 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-3.01_1, p5-LWP-MediaTypes-6.02_1, p5-LWP-Protocol-https-6.06_1, p5-List-MoreUtils-0.413, p5-MIME-Tools-5.506,2, p5-Mail-Tools-2.14, p5-Math-Derivative-0.03, p5-Math-Random-0.71_2, p5-Math-Spline-0.02_1, p5-Module-Build-0.4214, p5-Module-Pluggable-5.1_1, p5-Module-Runtime-0.014_1, p5-Moo-2.000002, p5-Mozilla-CA-20141217, p5-Net-HTTP-6.09, p5-Net-SSLeay-1.70, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_1, p5-Parse-RecDescent-1.967.009_2, p5-PostScript-0.06_2, p5-Role-Tiny-2.000001, p5-SOAP-Lite-1.14, p5-SVG-2.64, p5-SVG-Graph-0.04_1, p5-Scalar-List-Utils-1.42,1, p5-Set-Scalar-1.26_1, p5-Socket-2.020, 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-0.117_1, p5-Test-Differences-0.630,1, p5-Test-Exception-0.40, p5-Test-Most-0.34_1, p5-Test-NoWarnings-1.04_2, p5-Test-Simple-1.001.014, p5-Test-Warn-0.30_2, p5-Text-Diff-1.41_1, p5-Text-Iconv-1.7_2, 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-1.27, p5-Type-Tiny-1.000005_1, p5-Type-Tiny-XS-0.012_1, p5-Types-Serialiser-1.0_1, p5-URI-1.69, 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-2.0121,1, p5-XML-NamespaceSupport-1.11_1, p5-XML-Parser-2.44, p5-XML-Parser-Lite-0.72, 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-2.20_1, p5-XML-Twig-3.49, p5-XML-Writer-0.625_1, p5-XML-XPath-1.13_1, 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-3.73_1, p5-libwww-6.13, p5-libxml-0.08_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, printproto-1.0.5, python27-2.7.10, renderproto-0.11.1, tiff-4.0.4, 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-7.0.27
Also listed in: Perl5

paml-4.8a
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: jrm@ftfl.ca
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3

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-4.3.42, gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXaw-1.0.12_3,2, 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-1.1.4_3,1, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, printproto-1.0.5, xextproto-7.3.0, xproto-7.0.27

phyml-20121109
Simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69, autoconf-wrapper-20131203, automake-1.15, automake-wrapper-20131203, indexinfo-0.2.3, m4-1.4.17_1,1, perl5-5.20.2_6

platon-2015.03.30
Tool for viewing molecular/crystallographic structures
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, kbproto-1.0.6, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, mpc-1.0.3, mpfr-3.1.2_2, xproto-7.0.27

plink-1.07_4
Whole genome association analysis toolset
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: binutils-2.25.1, blas-3.5.0_3, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmake-4.1_2, gmp-5.1.3_2, indexinfo-0.2.3, lapack-3.5.0, mpc-1.0.3, mpfr-3.1.2_2
Also listed in: Science

plinkseq-0.10
Toolset for working with human genetic variation data
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3
Also listed in: Science

povchem-1.0_7
Simple yet powerful tool to generate POV from a PDB file
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, png-1.6.17_1, povray-meta-0.1, povray36-3.6.1_13, svgalib-1.4.3_7, tiff-4.0.4, xproto-7.0.27
Also listed in: Graphics

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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3

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-2.1.0_3, fixesproto-5.0, freeglut-2.8.1_4, inputproto-2.3.1, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libGL-10.4.6, libGLU-9.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_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-1.7.4_1,1, libXmu-1.1.2_3,1, libXrandr-1.4.2_3, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libglapi-10.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, pciids-20150731, png-1.6.17_1, randrproto-1.4.1, renderproto-0.11.1, tiff-4.0.4, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.27

psi88-1.0_8
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, mpc-1.0.3, mpfr-3.1.2_2

py27-biopython-1.65
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: binutils-2.25.1, blas-3.5.0_3, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, lapack-3.5.0, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.2_2, openblas-0.2.14,1, py27-numpy-1.9.2,1, py27-reportlab1-1.21.2_3, py27-setuptools27-17.0, python2-2_3, python27-2.7.10, suitesparse-4.0.2_4
Also listed in: Python

pycogent-1.5.3_3
Toolkit for statistical analysis of biological sequences
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: binutils-2.25.1, blas-3.5.0_3, cython-0.23, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, lapack-3.5.0, libedit-3.1.20150325_1, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.2_2, mysql56-client-5.6.26, openblas-0.2.14,1, postgresql93-client-9.3.9, py27-Babel-2.0, py27-Jinja2-2.8, py27-MarkupSafe-0.23, py27-MySQLdb-1.2.5, py27-alabaster-0.7.6, py27-docutils-0.12, py27-numpy-1.9.2,1, py27-psycopg2-2.6.1, py27-pygments-2.0.2, py27-pystemmer-1.3.0_1, py27-pytz-2015.4,1, py27-setuptools27-17.0, py27-six-1.9.0, py27-snowballstemmer-1.2.0_1, py27-sphinx-1.3.1_2, py27-sphinx_rtd_theme-0.1.8, py27-sqlalchemy06-0.6.9_1, py27-sqlite3-2.7.10_6, python2-2_3, python27-2.7.10, sqlite3-3.8.11.1, 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-2.25.1, blas-3.5.0_3, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, lapack-3.5.0, libffi-3.2.1, mpc-1.0.3, mpfr-3.1.2_2, openblas-0.2.14,1, py27-numpy-1.9.2,1, py27-setuptools27-17.0, python27-2.7.10, suitesparse-4.0.2_4
Also listed in: Python

python-nexus-0.87_1
Generic nexus file format reader for python
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: gettext-runtime-0.19.5.1, indexinfo-0.2.3, libffi-3.2.1, py27-setuptools27-17.0, python27-2.7.10
Also listed in: Python

raster3d-3.0.2_6
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ImageMagick-6.9.1.10_2,1, binutils-2.25.1, ca_root_nss-3.20, cairo-1.14.2,2, cups-client-2.0.3_2, cups-image-2.0.3_2, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gcc-4.8.5, gcc-ecj-4.5, gdk-pixbuf2-2.31.6, gettext-runtime-0.19.5.1, ghostscript9-base-9.06_11, ghostscript9-x11-9.06_11, giflib-5.0.6, glib-2.44.1_1, glproto-1.4.17, gmp-5.1.3_2, gnutls-3.3.17.1, graphite2-1.3.0, gsfonts-8.11_6, harfbuzz-1.0.1, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, jasper-1.900.1_15, jbig2dec-0.11_4, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, lcms2-2.7_1, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_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-1.7.4_1,1, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libcroco-0.6.8_2, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libfpx-1.3.1.4, libgcrypt-1.6.3, libgd-2.1.0_6,1, libglapi-10.4.6, libgpg-error-1.19_1, libgsf-1.14.34, libiconv-1.14_8, libidn-1.31, liblqr-1-0.4.1_8, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.13.3, libpthread-stubs-0.3_6, librsvg2-2.40.10, libtasn1-4.5_1, libwmf-0.2.8.4_14, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mDNSResponder-567, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpfr-3.1.2_2, nettle-2.7.1, openjpeg-2.1.0_1, p11-kit-0.23.1_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, pkgconf-0.9.12, png-1.6.17_1, python27-2.7.10, renderproto-0.11.1, svgalib-1.4.3_7, tiff-4.0.4, trousers-tddl-0.3.10_7, webp-0.4.3, 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-7.0.27
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

ruby21-bio-1.4.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: indexinfo-0.2.3, libedit-3.1.20150325_1, libffi-3.2.1, libyaml-0.1.6_2, ruby-2.1.6,1
Also listed in: Ruby

samtools-1.2
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.19.5.1, gmake-4.1_2, htslib-1.2.1, indexinfo-0.2.3

seaview-4.5.4.4
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-2.1.0_3, fixesproto-5.0, fltk-1.3.3_2, fontconfig-2.11.1,1, freetype2-2.6_1, gettext-runtime-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, jpeg-8_6, kbproto-1.0.6, libGL-10.4.6, libGLU-9.0.0_2, libX11-1.6.2_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-0.9.8_3, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libglapi-10.4.6, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, pciids-20150731, png-1.6.17_1, renderproto-0.11.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.27

seqan-1.3.1_3
C++ Sequence Analysis Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: binutils-2.25.1, ca_root_nss-3.20, cmake-3.2.3_2, cmake-modules-3.2.3, curl-7.44.0, expat-2.1.0_3, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, jsoncpp-0.6.0.r2_2, libarchive-3.1.2_4,1, libffi-3.2.1, lzo2-2.09, mpc-1.0.3, mpfr-3.1.2_2, python27-2.7.10

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-4.36
Tools for visualising sequence alignments
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: atk-2.16.0, binutils-2.25.1, ca_root_nss-3.20, cairo-1.14.2,2, compositeproto-0.4.2, cups-client-2.0.3_2, curl-7.44.0, damageproto-1.2.1, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gcc-4.8.5, gcc-ecj-4.5, gdk-pixbuf2-2.31.6, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, gmp-5.1.3_2, gnutls-3.3.17.1, graphite2-1.3.0, gtk-update-icon-cache-2.24.28, gtk2-2.24.28_1, harfbuzz-1.0.1, hicolor-icon-theme-0.15, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, jasper-1.900.1_15, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_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-1.7.4_1,1, libXinerama-1.1.3_3,1, libXrandr-1.4.2_3, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libgcrypt-1.6.3, libglapi-10.4.6, libgpg-error-1.19_1, libiconv-1.14_8, libidn-1.31, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libtasn1-4.5_1, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mDNSResponder-567, mkfontdir-1.0.7, mkfontscale-1.1.2, mpc-1.0.3, mpfr-3.1.2_2, nettle-2.7.1, p11-kit-0.23.1_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, pkgconf-0.9.12, png-1.6.17_1, python-2.7_2,2, python2-2_3, python27-2.7.10, randrproto-1.4.1, renderproto-0.11.1, shared-mime-info-1.4, sqlite3-3.8.11.1, tiff-4.0.4, trousers-tddl-0.3.10_7, 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-7.0.27

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

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-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmake-4.1_2, gmp-5.1.3_2, indexinfo-0.2.3, mpc-1.0.3, mpfr-3.1.2_2

tRNAscan-SE-1.23_1
Improved tool for transfer RNA detection
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.20.2_6

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-2.25.1, clustalw-2.1_1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, mpc-1.0.3, mpfr-3.1.2_2

tinker-7.1.3
General purpose molecular modelling package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.25.1, gcc-4.8.5, gcc-ecj-4.5, gettext-runtime-0.19.5.1, gmp-5.1.3_2, indexinfo-0.2.3, mpc-1.0.3, mpfr-3.1.2_2

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_1
Phylogenetic tree viewer
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_1, atk-2.16.0, ca_root_nss-3.20, cairo-1.14.2,2, compositeproto-0.4.2, cups-client-2.0.3_2, damageproto-1.2.1, dbus-1.8.20, dbus-glib-0.104, dconf-0.24.0, dejavu-2.35, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gconf2-3.2.6_4, gdk-pixbuf2-2.31.6, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, gmake-4.1_2, gmp-5.1.3_2, gnome_subr-1.0, gnutls-3.3.17.1, gobject-introspection-1.44.0, graphite2-1.3.0, gstreamer-0.10.36_4, gstreamer-plugins-0.10.36_6,3, gtk-update-icon-cache-2.24.28, gtk2-2.24.28_1, harfbuzz-1.0.1, hicolor-icon-theme-0.15, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, jasper-1.900.1_15, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, libEGL-10.4.6, libGL-10.4.6, libGLU-9.0.0_2, libICE-1.0.9_1,1, libIDL-0.8.14_2, libSM-1.2.2_3,1, libX11-1.6.2_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-1.7.4_1,1, libXinerama-1.1.3_3,1, libXrandr-1.4.2_3, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXv-1.0.10_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libgcrypt-1.6.3, libglapi-10.4.6, libgpg-error-1.19_1, libiconv-1.14_8, libidn-1.31, libmspack-0.5, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libtasn1-4.5_1, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mDNSResponder-567, mkfontdir-1.0.7, mkfontscale-1.1.2, nettle-2.7.1, nspr-4.10.9, orc-0.4.24_1, p11-kit-0.23.1_1, pango-1.36.8_2, pangox-compat-0.0.2_1, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, polkit-0.113, python-2.7_2,2, python2-2_3, python27-2.7.10, randrproto-1.4.1, renderproto-0.11.1, shared-mime-info-1.4, spidermonkey170-17.0.0_1, tiff-4.0.4, trousers-tddl-0.3.10_7, videoproto-2.3.2, wx28-gtk2-common-2.8.12_5, wx28-gtk2-contrib-common-2.8.12_5, wx28-gtk2-unicode-2.8.12_5, wx28-gtk2-unicode-contrib-2.8.12_5, 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-7.0.27

ugene-1.17.0_1
Free, open-source, cross-platform bioinformatics toolkit
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: atk-2.16.0, bash-4.3.42, ca_root_nss-3.20, cairo-1.14.2,2, compositeproto-0.4.2, damageproto-1.2.1, dejavu-2.35, desktop-file-utils-0.22_3, dri2proto-2.8, encodings-1.0.4_3,1, expat-2.1.0_3, 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-2.11.1,1, freetype2-2.6_1, gdk-pixbuf2-2.31.6, gettext-runtime-0.19.5.1, glib-2.44.1_1, glproto-1.4.17, gobject-introspection-1.44.0, graphite2-1.3.0, gstreamer-0.10.36_4, gstreamer-plugins-0.10.36_6,3, gtk-update-icon-cache-2.24.28, harfbuzz-1.0.1, hicolor-icon-theme-0.15, icu-55.1, indexinfo-0.2.3, inputproto-2.3.1, jasper-1.900.1_15, jbigkit-2.1_1, jpeg-8_6, kbproto-1.0.6, lcms-1.19_6,1, libEGL-10.4.6, libGL-10.4.6, libGLU-9.0.0_2, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_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, libXfontcache-1.0.5_3, libXft-2.3.2_1, libXi-1.7.4_1,1, libXinerama-1.1.3_3,1, libXmu-1.1.2_3,1, libXrandr-1.4.2_3, libXrender-0.9.8_3, libXt-1.1.4_3,1, libXtst-1.2.2_3, libXv-1.0.10_3,1, libXxf86vm-1.1.4_1, libdevq-0.0.2_1, libdrm-2.4.60,1, libffi-3.2.1, libfontenc-1.1.2_3, libglapi-10.4.6, libiconv-1.14_8, libmng-1.0.10_2, libpciaccess-0.13.3, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, libxshmfence-1.2, mkfontdir-1.0.7, mkfontscale-1.1.2, orc-0.4.24_1, pango-1.36.8_2, pciids-20150731, pcre-8.37_4, perl5-5.20.2_6, pixman-0.32.6_1, png-1.6.17_1, python2-2_3, python27-2.7.10, qt4-corelib-4.8.6_5, qt4-declarative-4.8.6_2, qt4-gui-4.8.6_5, qt4-imageformats-4.8.6_3, qt4-linguisttools-4.8.6, qt4-moc-4.8.6, qt4-network-4.8.6_1, qt4-opengl-4.8.6_2, qt4-qmake-4.8.6, qt4-rcc-4.8.6, qt4-script-4.8.6_1, qt4-scripttools-4.8.6_1, qt4-sql-4.8.6_1, qt4-svg-4.8.6_1, qt4-testlib-4.8.6_1, qt4-uic-4.8.6, qt4-webkit-4.8.6_2, qt4-xml-4.8.6_1, qt4-xmlpatterns-4.8.6_1, randrproto-1.4.1, recordproto-1.14.2, renderproto-0.11.1, shared-mime-info-1.4, tiff-4.0.4, videoproto-2.3.2, xcb-util-0.4.0_1,1, xcb-util-renderutil-0.3.9_1, xdg-utils-1.0.2.20130919_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xprop-1.2.2, xproto-7.0.27, xset-1.2.3_1
Also listed in: Science

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-0.19.5.1, gmake-4.1_2, indexinfo-0.2.3, libffi-3.2.1, perl5-5.20.2_6, python27-2.7.10

wise-2.4.1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.5.1, glib-2.44.1_1, indexinfo-0.2.3, libffi-3.2.1, libiconv-1.14_8, pcre-8.37_4, perl5-5.20.2_6, pkgconf-0.9.12, python27-2.7.10

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-0.19.5.1, glib12-1.2.10_15, gmake-4.1_2, gtk12-1.2.10_24, indexinfo-0.2.3, inputproto-2.3.1, kbproto-1.0.6, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.2_3,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.1_3, libXi-1.7.4_1,1, libpthread-stubs-0.3_6, libxcb-1.11_1, libxml2-2.9.2_3, xextproto-7.3.0, xproto-7.0.27

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