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FreeBSD Ports: Biology

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Biologie-Software.

InsightToolkit-2.8.1_2
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.17, cmake-3.0.2, cmake-modules-3.0.2, curl-7.38.0_1, expat-2.1.0_1
Also listed in: Science

afni-2012.04.17.2129_11
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: R-3.0.2_3, binutils-2.24_1, ca_root_nss-3.17, cairo-1.12.16_1,2, cups-client-1.7.3_2, cups-image-1.7.3_1, curl-7.38.0_1, damageproto-1.2.1, dejavu-2.34_4, dri2proto-2.8, encodings-1.0.4_1,1, endian-1.1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, ghostscript9-9.06_8, glib-2.36.3_4, glproto-1.4.17, gmake-3.82_1, gmp-5.1.3_2, gnomehier-3.0, graphite2-1.2.4, gsed-4.2.2, gsfonts-8.11_6, gsl-1.16_2, harfbuzz-0.9.28, hdf-szip-2.1_2, hdf5-1.8.13_1, icu-53.1, indexinfo-0.2, inputproto-2.3.1, jasper-1.900.1_14, jbig2dec-0.11_2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, lcms2-2.6_3, libGL-9.1.7_2, libGLU-9.0.0_2, libGLw-8.0.0_2, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXScrnSaver-1.2.2_2, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libglapi-9.1.7_1, libiconv-1.14_4, libidn-1.28_2, libpaper-1.1.24.3, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mpc-1.0.2_1, mpeg_encode-1.5b, mpfr-3.1.2_2, netcdf-4.3.2, netcdf-fortran-4.4.1, netpbm-10.35.92_1, open-motif-2.3.4_1, pango-1.34.1_7, pciids-20140916, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, printproto-1.0.5, python27-2.7.8_5, qhull5-1.0_3, renderproto-0.11.1, scrnsaverproto-1.2.2, svgalib-1.4.3_7, tcl86-8.6.2_1, tiff-4.0.3_4, tk86-8.6.2, whirlgif-3.04, xbitmaps-1.1.1, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26
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-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4

artemis-9_1
DNA sequence viewer and annotation tool
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.0.28, dejavu-2.34_4, expat-2.1.0_1, fixesproto-5.0, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, inputproto-2.3.1, java-zoneinfo-2014.f, javavmwrapper-2.5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXi-1.7.4,1, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXtst-1.2.2_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, openjdk-7.65.17,1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.26
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-3.17, cmake-3.0.2, cmake-modules-3.0.2, curl-7.38.0_1, expat-2.1.0_1

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

biococoa-2.2.2_1
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: theraven@FreeBSD.org
Requires: avahi-app-0.6.31_3, binutils-2.24_1, ca_root_nss-3.17, cairo-1.12.16_1,2, cups-client-1.7.3_2, damageproto-1.2.1, dbus-1.8.8, dbus-glib-0.100.2_1, dri2proto-2.8, expat-2.1.0_1, fixesproto-5.0, flac-1.3.0_2, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gdbm-1.11_2, gettext-0.18.3.1_1, giflib-nox11-4.2.3_3, glib-2.36.3_4, gmake-3.82_1, gmp-5.1.3_2, gnome_subr-1.0, gnomehier-3.0, gnustep-back-0.24.0_4, gnustep-base-1.24.6_5, gnustep-gui-0.24.0_2, gnustep-make-2.6.6, gnutls-3.2.16_5, gobject-introspection-1.36.0_3, icu-53.1, indexinfo-0.2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXxf86vm-1.1.3_2, libao-1.2.0_1, libdaemon-0.14_1, libdrm-2.4.52_1,1, libffi-3.0.13_2, libgcrypt-1.6.1_5, libglapi-9.1.7_1, libgpg-error-1.15, libiconv-1.14_4, libidn-1.28_2, libobjc2-1.7_1, libogg-1.3.2,4, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libsndfile-1.0.25_4, libtasn1-4.2, libvorbis-1.3.4_1,3, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, libxslt-1.1.28_4, mpc-1.0.2_1, mpfr-3.1.2_2, nettle-2.7.1, p11-kit-0.20.3_1, pciids-20140916, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, python2-2_3, python27-2.7.8_5, renderproto-0.11.1, tiff-4.0.3_4, trousers-tddl-0.3.10_7, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.26
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-1.0.28, apache-ant-1.9.4, dejavu-2.34_4, expat-2.1.0_1, fixesproto-5.0, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, inputproto-2.3.1, java-zoneinfo-2014.f, javavmwrapper-2.5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXi-1.7.4,1, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXtst-1.2.2_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, openjdk-7.65.17,1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.26
Also listed in: Java

blat-35
Fast tool for local sequence similarity searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4, png-1.5.18

boinc-simap-5.10.5.09_7
Similarity Matrix of Proteins project for BOINC
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_1, atk-2.8.0_1, binutils-2.24_1, boinc-client-7.2.33_5, ca_root_nss-3.17, cairo-1.12.16_1,2, compat6x-i386-6.4.604000.200810_3, compositeproto-0.4.2, cups-client-1.7.3_2, curl-7.38.0_1, damageproto-1.2.1, dbus-1.8.8, dbus-glib-0.100.2_1, dconf-0.14.1_1, dejavu-2.34_4, dri2proto-2.8, encodings-1.0.4_1,1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freeglut-2.8.1_3, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gconf2-2.32.0_6, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, glib-2.36.3_4, gmp-5.1.3_2, gnome_subr-1.0, gnomehier-3.0, gobject-introspection-1.36.0_3, graphite2-1.2.4, gstreamer-0.10.36_2, gstreamer-plugins-0.10.36_4,3, gtk-update-icon-cache-2.24.22, gtk2-2.24.22_4, harfbuzz-0.9.28, hicolor-icon-theme-0.12, icu-53.1, indexinfo-0.2, inputproto-2.3.1, jasper-1.900.1_14, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libICE-1.0.9,1, libIDL-0.8.14_2, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXmu-1.1.2_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXv-1.0.10_2,1, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libglapi-9.1.7_1, libiconv-1.14_4, libmspack-0.4_2, libnotify-0.7.5_1, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, orc-0.4.21, pango-1.34.1_7, pangox-compat-0.0.2_1, pciids-20140916, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, polkit-0.105_3, python-2.7_2,2, python2-2_3, python27-2.7.8_5, randrproto-1.4.0, renderproto-0.11.1, shared-mime-info-1.1_1, sqlite3-3.8.6, tiff-4.0.3_4, videoproto-2.3.2, wx28-gtk2-common-2.8.12_4, wx28-gtk2-unicode-2.8.12_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26

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-0.18.3.1_1, indexinfo-0.2, libiconv-1.14_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-f10-expat-2.0.1, linux-f10-fontconfig-2.6.0, linux-f10-xorg-libs-7.4_1, linux_base-f10-10_7, perl5-5.16.3_11, 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-2.24_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmake-3.82_1, gmp-5.1.3_2, indexinfo-0.2, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2, python27-2.7.8_5
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-2.8.0_1, binutils-2.24_1, ca_root_nss-3.17, cairo-1.12.16_1,2, cantarell-fonts-0.0.15, compositeproto-0.4.2, cups-client-1.7.3_2, curl-7.38.0_1, damageproto-1.2.1, dbus-1.8.8, dbus-glib-0.100.2_1, dconf-0.14.1_1, dejavu-2.34_4, dri2proto-2.8, enchant-1.6.0_4, encodings-1.0.4_1,1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gconf2-2.32.0_6, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, glib-2.36.3_4, glib-networking-2.36.2_4, gmp-5.1.3_2, gnome_subr-1.0, gnomehier-3.0, gnutls-3.2.16_5, gobject-introspection-1.36.0_3, graphite2-1.2.4, gsettings-desktop-schemas-3.6.1_1, gstreamer-0.10.36_2, gstreamer-plugins-0.10.36_4,3, gtk-update-icon-cache-2.24.22, gtk2-2.24.22_4, harfbuzz-0.9.28, hicolor-icon-theme-0.12, hunspell-1.3.3, icu-53.1, indexinfo-0.2, inputproto-2.3.1, jasper-1.900.1_14, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libICE-1.0.9,1, libIDL-0.8.14_2, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXv-1.0.10_2,1, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libgcrypt-1.6.1_5, libglapi-9.1.7_1, libgpg-error-1.15, libiconv-1.14_4, libidn-1.28_2, libmspack-0.4_2, libpciaccess-0.13.2_2, libproxy-0.4.6, libpthread-stubs-0.3_6, libsoup-2.40.3_6, libtasn1-4.2, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, libxslt-1.1.28_4, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, nettle-2.7.1, orc-0.4.21, p11-kit-0.20.3_1, pango-1.34.1_7, pciids-20140916, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, polkit-0.105_3, py27-setuptools27-5.5.1, py27-wxPython-common-3.0.0.0_1, py27-wxPython30-3.0.0.0_1, python-2.7_2,2, python2-2_3, python27-2.7.8_5, randrproto-1.4.0, renderproto-0.11.1, shared-mime-info-1.1_1, sqlite3-3.8.6, tiff-4.0.3_4, trousers-tddl-0.3.10_7, videoproto-2.3.2, webkit-gtk2-1.8.3_6, wx30-gtk2-3.0.1_2, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26
Also listed in: Deskutils, Python

emboss-6.6.0
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_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libgd-2.1.0_4,1, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, open-motif-2.3.4_1, png-1.5.18, primer3-2.3.6, printproto-1.0.5, renderproto-0.11.1, tiff-4.0.3_4, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.26

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

fasta3-36.3.6d_1
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-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, kbproto-1.0.6, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, xproto-7.0.26

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-4.3.24, gawk-4.1.1_1, gettext-0.18.3.1_1, indexinfo-0.2, libiconv-1.14_4, 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-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4, perl5-5.16.3_11

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-2.8.0_1, cairo-1.12.16_1,2, compositeproto-0.4.2, cups-client-1.7.3_2, damageproto-1.2.1, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, gtk-update-icon-cache-2.24.22, gtk2-2.24.22_4, harfbuzz-0.9.28, hicolor-icon-theme-0.12, icu-53.1, indexinfo-0.2, inputproto-2.3.1, intltool-0.50.2, jasper-1.900.1_14, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, p5-XML-Parser-2.41_1, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, pkgconf-0.9.6_1, png-1.5.18, python-2.7_2,2, python2-2_3, python27-2.7.8_5, randrproto-1.4.0, renderproto-0.11.1, shared-mime-info-1.1_1, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4

hmmer-3.0
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.16.3_11

io_lib-1.13.7
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: ca_root_nss-3.17, curl-7.38.0_1, gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_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-1.0.28, apache-ant-1.9.4, dejavu-2.34_4, expat-2.1.0_1, fixesproto-5.0, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, inputproto-2.3.1, java-zoneinfo-2014.f, javavmwrapper-2.5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXi-1.7.4,1, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXtst-1.2.2_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, openjdk-7.65.17,1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.26
Also listed in: Java

lagan-2.0
Efficient tools for large-scale multiple alignments of genomic DNA
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.16.3_11

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

libsbml-5.10.2
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.17, cmake-3.0.2, cmake-modules-3.0.2, curl-7.38.0_1, expat-2.1.0_1, libiconv-1.14_4, libxml2-2.9.1_1
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-f10-10_7

mafft-7.149
Multiple alignment program for amino acid or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_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-3.5.1
Program to estimate population sizes and migration rates
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org

minc2-2.2.00
Medical Imaging NetCDF
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69, autoconf-wrapper-20131203, automake-1.14, automake-wrapper-20131203, bash-4.3.24, bison-2.7.1,1, ca_root_nss-3.17, curl-7.38.0_1, gettext-0.18.3.1_1, gmake-3.82_1, hdf-szip-2.1_2, hdf5-1.8.13_1, indexinfo-0.2, libiconv-1.14_4, libtool-2.4.2_3, m4-1.4.17_1,1, netcdf-4.3.2, perl5-5.16.3_11
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-2.24_1, damageproto-1.2.1, dri2proto-2.8, expat-2.1.0_1, fixesproto-5.0, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, glproto-1.4.17, gmake-3.82_1, gmp-5.1.3_2, indexinfo-0.2, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libglapi-9.1.7_1, libiconv-1.14_4, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mpc-1.0.2_1, mpfr-3.1.2_2, pciids-20140916, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.26

mopac-7.1.11_4
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69, autoconf-wrapper-20131203, automake-1.14, automake-wrapper-20131203, f2c-20060810_4, gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4, libtool-2.4.2_3, m4-1.4.17_1,1, perl5-5.16.3_11

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-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_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-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4, perl5-5.16.3_11

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-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_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, open-motif-2.3.4_1, png-1.5.18, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.26

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_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, ncbi-toolkit-2012.06.20, open-motif-2.3.4_1, png-1.5.18, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.1, xextproto-7.3.0, xproto-7.0.26

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-2.24_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2

p5-AcePerl-1.92_2
Perl5 interface to the ACEDB genome database system
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: p5-Cache-2.06, p5-Cache-Cache-1.06, p5-Digest-SHA1-2.13, p5-Error-0.17022, p5-File-NFSLock-1.21, p5-Heap-0.80, p5-IO-String-1.08, p5-IPC-ShareLite-0.17, p5-TimeDate-2.30_1,1, perl5-5.16.3_11
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.091
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: perl5-5.16.3_11
Also listed in: Perl5

p5-Bio-Das-1.17_2
Client-side library for Distributed Genome Annotation System
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.12.16_1,2, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, graphviz-2.38.0_1, harfbuzz-0.9.28, icu-53.1, indexinfo-0.2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libgd-2.1.0_4,1, libiconv-1.14_4, libltdl-2.4.2_3, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mysql55-client-5.5.39, p5-Algorithm-C3-0.10, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Carp-1.33.01, p5-Class-AutoClass-1.56, p5-Class-C3-0.27, p5-Class-Data-Inheritable-0.08, p5-Class-Inspector-1.28, p5-Class-Load-0.21, p5-Class-Load-XS-0.08, p5-Clone-0.35, p5-Convert-BinHex-1.123, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.72, p5-DBD-mysql-4.028, p5-DBI-1.631, p5-Data-OptList-0.109, p5-Data-Stag-0.14_1, p5-Devel-GlobalDestruction-0.13, p5-Devel-StackTrace-1.34, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.9, p5-Dist-CheckConflicts-0.11, p5-Email-Date-Format-1.004, p5-Encode-Locale-1.03, p5-Error-0.17022, p5-Eval-Closure-0.11, p5-Exception-Class-1.38, p5-File-Listing-6.04, p5-File-Slurp-Tiny-0.003, p5-File-Temp-0.23.04, p5-GD-2.53, p5-GD-SVG-0.33_5, p5-Graph-0.96,1, p5-GraphViz-2.15, p5-HTML-Element-Extended-1.18, p5-HTML-Parser-3.71, p5-HTML-TableExtract-2.11, p5-HTML-Tagset-3.20, p5-HTML-Tree-5.03, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-Hash-AutoHash-1.17, p5-Hash-AutoHash-Args-1.18, p5-Heap-0.80, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-IO-String-1.08, p5-IO-Tty-1.12, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.06, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.03.0, p5-MIME-Tools-5.505,2, p5-MIME-Types-2.08, p5-MRO-Compat-0.12, p5-Mail-Tools-2.13, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.02, p5-Module-Implementation-0.09, p5-Module-Runtime-0.014, p5-Moose-2.1204,1, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.36, p5-Package-Stash-XS-0.28, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-Path-Class-0.34, p5-PathTools-3.4700, p5-PostScript-0.06, p5-SOAP-Lite-0.716, p5-SVG-2.59, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.35,1, p5-Set-Scalar-1.26, p5-Socket-2.015, p5-Sort-Naturally-1.03, p5-Spreadsheet-ParseExcel-0.65,1, p5-Statistics-Descriptive-3.0605, p5-Sub-Exporter-0.987, p5-Sub-Exporter-Progressive-0.001.011, p5-Sub-Install-0.928, p5-Sub-Name-0.05, p5-Sub-Uplevel-0.2400, p5-Task-Weaken-1.04, p5-Test-Deep-0.113, p5-Test-Differences-0.620,1, p5-Test-Exception-0.32, p5-Test-Most-0.33, p5-Test-NoWarnings-1.04_1, p5-Test-Tester-0.10.9, p5-Test-Warn-0.30, p5-Text-Diff-1.41, p5-Text-Iconv-1.7_1, p5-Text-Shellwords-1.08, p5-Text-Tabs+Wrap-2013.0523, p5-Tie-IxHash-1.23, p5-Tie-ToObject-0.03_1, p5-TimeDate-2.30_1,1, p5-Tree-DAG_Node-1.22, p5-Try-Tiny-0.18, p5-URI-1.64, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41_1, p5-XML-RegExp-0.04, p5-XML-SAX-0.99_1, p5-XML-SAX-Base-1.08, p5-XML-SAX-Expat-0.51, p5-XML-SAX-Writer-0.54, p5-XML-Simple-2.20, p5-XML-Twig-3.48, p5-XML-Writer-0.625, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.14, p5-YAML-1.11, p5-bioperl-1.6.924, p5-libwww-6.08, p5-libxml-0.08, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, printproto-1.0.5, python27-2.7.8_5, renderproto-0.11.1, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xorg-fonts-truetype-7.7_1, xproto-7.0.26
Also listed in: Perl5

p5-Bio-Das-Lite-2.11
Perl extension for the DAS (HTTP+XML) Protocol
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.17, curl-7.38.0_1, p5-Authen-NTLM-1.09, p5-Digest-HMAC-1.03, p5-Encode-Locale-1.03, p5-File-Listing-6.04, p5-HTML-Parser-3.71, p5-HTML-Tagset-3.20, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-LWP-MediaTypes-6.02, p5-Module-Build-0.4206, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-Readonly-2.00, p5-Socket-2.015, p5-URI-1.64, p5-WWW-Curl-4.17, p5-WWW-RobotRules-6.02, p5-libwww-6.08, perl5-5.16.3_11
Also listed in: Perl5

p5-Bio-GFF3-2.0_1
Fast low-level functions for parsing and formatting GFF3
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-File-ReadBackwards-1.05, p5-List-MoreUtils-0.33, p5-URI-1.64, perl5-5.16.3_11
Also listed in: Perl5

p5-Bio-Glite-0.10_1
Perl Interface to G-language
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Authen-NTLM-1.09, p5-Digest-HMAC-1.03, p5-Encode-Locale-1.03, p5-File-Listing-6.04, p5-HTML-Parser-3.71, p5-HTML-Tagset-3.20, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-LWP-MediaTypes-6.02, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-Socket-2.015, p5-URI-1.64, p5-WWW-RobotRules-6.02, p5-libwww-6.08, perl5-5.16.3_11
Also listed in: Perl5

p5-Bio-Graphics-2.38
Generate GD Images of Bio::Seq Objects
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.17, cairo-1.12.16_1,2, curl-7.38.0_1, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, graphviz-2.38.0_1, harfbuzz-0.9.28, icu-53.1, indexinfo-0.2, io_lib-1.13.7, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libgd-2.1.0_4,1, libiconv-1.14_4, libltdl-2.4.2_3, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mysql55-client-5.5.39, p5-Algorithm-C3-0.10, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Bio-SCF-1.03, p5-Carp-1.33.01, p5-Class-AutoClass-1.56, p5-Class-C3-0.27, p5-Class-Data-Inheritable-0.08, p5-Class-Inspector-1.28, p5-Class-Load-0.21, p5-Class-Load-XS-0.08, p5-Clone-0.35, p5-Convert-BinHex-1.123, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.72, p5-DBD-mysql-4.028, p5-DBI-1.631, p5-Data-OptList-0.109, p5-Data-Stag-0.14_1, p5-Devel-GlobalDestruction-0.13, p5-Devel-StackTrace-1.34, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.9, p5-Dist-CheckConflicts-0.11, p5-Email-Date-Format-1.004, p5-Encode-Locale-1.03, p5-Error-0.17022, p5-Eval-Closure-0.11, p5-Exception-Class-1.38, p5-File-Listing-6.04, p5-File-Slurp-Tiny-0.003, p5-File-Temp-0.23.04, p5-GD-2.53, p5-GD-SVG-0.33_5, p5-Graph-0.96,1, p5-GraphViz-2.15, p5-HTML-Element-Extended-1.18, p5-HTML-Parser-3.71, p5-HTML-TableExtract-2.11, p5-HTML-Tagset-3.20, p5-HTML-Tree-5.03, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-Hash-AutoHash-1.17, p5-Hash-AutoHash-Args-1.18, p5-Heap-0.80, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-IO-String-1.08, p5-IO-Tty-1.12, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.06, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.03.0, p5-MIME-Tools-5.505,2, p5-MIME-Types-2.08, p5-MRO-Compat-0.12, p5-Mail-Tools-2.13, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.02, p5-Module-Build-0.4206, p5-Module-Implementation-0.09, p5-Module-Runtime-0.014, p5-Moose-2.1204,1, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.36, p5-Package-Stash-XS-0.28, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-Path-Class-0.34, p5-PathTools-3.4700, p5-PostScript-0.06, p5-SOAP-Lite-0.716, p5-SVG-2.59, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.35,1, p5-Set-Scalar-1.26, p5-Socket-2.015, p5-Sort-Naturally-1.03, p5-Spreadsheet-ParseExcel-0.65,1, p5-Statistics-Descriptive-3.0605, p5-Sub-Exporter-0.987, p5-Sub-Exporter-Progressive-0.001.011, p5-Sub-Install-0.928, p5-Sub-Name-0.05, p5-Sub-Uplevel-0.2400, p5-Task-Weaken-1.04, p5-Test-Deep-0.113, p5-Test-Differences-0.620,1, p5-Test-Exception-0.32, p5-Test-Most-0.33, p5-Test-NoWarnings-1.04_1, p5-Test-Tester-0.10.9, p5-Test-Warn-0.30, p5-Text-Diff-1.41, p5-Text-Iconv-1.7_1, p5-Text-Shellwords-1.08, p5-Text-Tabs+Wrap-2013.0523, p5-Tie-IxHash-1.23, p5-Tie-ToObject-0.03_1, p5-TimeDate-2.30_1,1, p5-Tree-DAG_Node-1.22, p5-Try-Tiny-0.18, p5-URI-1.64, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41_1, p5-XML-RegExp-0.04, p5-XML-SAX-0.99_1, p5-XML-SAX-Base-1.08, p5-XML-SAX-Expat-0.51, p5-XML-SAX-Writer-0.54, p5-XML-Simple-2.20, p5-XML-Twig-3.48, p5-XML-Writer-0.625, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.14, p5-YAML-1.11, p5-bioperl-1.6.924, p5-libwww-6.08, p5-libxml-0.08, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, printproto-1.0.5, python27-2.7.8_5, renderproto-0.11.1, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xorg-fonts-truetype-7.7_1, xproto-7.0.26
Also listed in: Perl5

p5-Bio-MAGETAB-1.31
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, p5-B-Hooks-EndOfScope-0.13, p5-Carp-Clan-6.04, p5-Class-C3-0.27, p5-Class-Load-0.21, p5-Class-Load-XS-0.08, p5-Class-Singleton-1.4, p5-Data-OptList-0.109, p5-Date-Manip-6.46, p5-DateTime-1.12, p5-DateTime-Format-DateManip-0.04, p5-DateTime-Locale-0.45, p5-DateTime-TimeZone-1.74, p5-Devel-GlobalDestruction-0.13, p5-Devel-StackTrace-1.34, p5-Digest-HMAC-1.03, p5-Dist-CheckConflicts-0.11, p5-Email-Valid-1.192, p5-Eval-Closure-0.11, p5-IO-Socket-INET6-2.69, p5-List-AllUtils-0.08_1, p5-List-MoreUtils-0.33, p5-MRO-Compat-0.12, p5-Mail-Tools-2.13, p5-Module-Implementation-0.09, p5-Module-Runtime-0.014, p5-Moose-2.1204,1, p5-MooseX-FollowPBP-0.05, p5-MooseX-Types-0.44, p5-Net-DNS-0.79, p5-Net-Domain-TLD-1.72, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.36, p5-Package-Stash-XS-0.28, p5-Params-Coerce-0.14_1, p5-Params-Util-1.07, p5-Params-Validate-1.13, p5-Parse-RecDescent-1.967.009_1, p5-Scalar-List-Utils-1.35,1, p5-Socket6-0.25_1, p5-Sub-Exporter-0.987, p5-Sub-Exporter-Progressive-0.001.011, p5-Sub-Identify-0.07, p5-Sub-Install-0.928, p5-Sub-Name-0.05, p5-Task-Weaken-1.04, p5-Text-CSV_XS-1.02, p5-TimeDate-2.30_1,1, p5-Try-Tiny-0.18, p5-URI-1.64, p5-YAML-Syck-1.27, p5-namespace-autoclean-0.20, p5-namespace-clean-0.25, perl5-5.16.3_11
Also listed in: Perl5

p5-Bio-NEXUS-0.78
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, perl5-5.16.3_11
Also listed in: Perl5

p5-Bio-Phylo-0.56
Phylogenetic analysis using Perl
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.12.16_1,2, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, graphviz-2.38.0_1, harfbuzz-0.9.28, icu-53.1, indexinfo-0.2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libgd-2.1.0_4,1, libiconv-1.14_4, libltdl-2.4.2_3, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mysql55-client-5.5.39, p5-Algorithm-C3-0.10, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Carp-1.33.01, p5-Class-AutoClass-1.56, p5-Class-C3-0.27, p5-Class-Data-Inheritable-0.08, p5-Class-Inspector-1.28, p5-Class-Load-0.21, p5-Class-Load-XS-0.08, p5-Clone-0.35, p5-Convert-BinHex-1.123, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.72, p5-DBD-mysql-4.028, p5-DBI-1.631, p5-Data-OptList-0.109, p5-Data-Stag-0.14_1, p5-Data-TemporaryBag-0.09, p5-Devel-GlobalDestruction-0.13, p5-Devel-StackTrace-1.34, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.9, p5-Dist-CheckConflicts-0.11, p5-Email-Date-Format-1.004, p5-Encode-Locale-1.03, p5-Error-0.17022, p5-Eval-Closure-0.11, p5-Exception-Class-1.38, p5-File-Listing-6.04, p5-File-Slurp-Tiny-0.003, p5-File-Temp-0.23.04, p5-Font-TTF-1.04, p5-GD-2.53, p5-GD-SVG-0.33_5, p5-Graph-0.96,1, p5-GraphViz-2.15, p5-HTML-Element-Extended-1.18, p5-HTML-Parser-3.71, p5-HTML-TableExtract-2.11, p5-HTML-Tagset-3.20, p5-HTML-Tree-5.03, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-Hash-AutoHash-1.17, p5-Hash-AutoHash-Args-1.18, p5-Heap-0.80, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-IO-String-1.08, p5-IO-Tty-1.12, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.06, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.03.0, p5-MIME-Tools-5.505,2, p5-MIME-Types-2.08, p5-MRO-Compat-0.12, p5-Mail-Tools-2.13, p5-Math-Bezier-Convert-0.02, p5-Math-CDF-0.1, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.02, p5-Module-Implementation-0.09, p5-Module-Runtime-0.014, p5-Moose-2.1204,1, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-OLE-Storage_Lite-0.19, p5-PDF-API2-2.022, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.36, p5-Package-Stash-XS-0.28, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-Path-Class-0.34, p5-PathTools-3.4700, p5-PostScript-0.06, p5-SOAP-Lite-0.716, p5-SVG-2.59, p5-SVG-Graph-0.04, p5-SWF-Builder-0.16, p5-SWF-File-0.42_1,1, p5-Scalar-List-Utils-1.35,1, p5-Set-Scalar-1.26, p5-Socket-2.015, p5-Sort-Naturally-1.03, p5-Spreadsheet-ParseExcel-0.65,1, p5-Statistics-Descriptive-3.0605, p5-Sub-Exporter-0.987, p5-Sub-Exporter-Progressive-0.001.011, p5-Sub-Install-0.928, p5-Sub-Name-0.05, p5-Sub-Uplevel-0.2400, p5-Task-Weaken-1.04, p5-Test-Deep-0.113, p5-Test-Differences-0.620,1, p5-Test-Exception-0.32, p5-Test-Most-0.33, p5-Test-NoWarnings-1.04_1, p5-Test-Tester-0.10.9, p5-Test-Warn-0.30, p5-Text-Diff-1.41, p5-Text-Iconv-1.7_1, p5-Text-Shellwords-1.08, p5-Text-Tabs+Wrap-2013.0523, p5-Tie-IxHash-1.23, p5-Tie-ToObject-0.03_1, p5-TimeDate-2.30_1,1, p5-Tree-DAG_Node-1.22, p5-Try-Tiny-0.18, p5-URI-1.64, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-LibXML-2.0116,1, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41_1, p5-XML-RegExp-0.04, p5-XML-SAX-0.99_1, p5-XML-SAX-Base-1.08, p5-XML-SAX-Expat-0.51, p5-XML-SAX-Writer-0.54, p5-XML-Simple-2.20, p5-XML-Twig-3.48, p5-XML-Writer-0.625, p5-XML-XML2JSON-0.06, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.14, p5-YAML-1.11, p5-YAML-Syck-1.27, p5-bioperl-1.6.924, p5-libwww-6.08, p5-libxml-0.08, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, printproto-1.0.5, python27-2.7.8_5, renderproto-0.11.1, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xorg-fonts-truetype-7.7_1, xproto-7.0.26
Also listed in: Perl5

p5-Bio-SCF-1.03
Read and Update SCF Chromatographic Sequence Files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: ca_root_nss-3.17, curl-7.38.0_1, io_lib-1.13.7, perl5-5.16.3_11
Also listed in: Perl5

p5-bioperl-1.6.924
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.12.16_1,2, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, graphviz-2.38.0_1, harfbuzz-0.9.28, icu-53.1, indexinfo-0.2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libgd-2.1.0_4,1, libiconv-1.14_4, libltdl-2.4.2_3, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mysql55-client-5.5.39, p5-Algorithm-C3-0.10, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Carp-1.33.01, p5-Class-AutoClass-1.56, p5-Class-C3-0.27, p5-Class-Data-Inheritable-0.08, p5-Class-Inspector-1.28, p5-Class-Load-0.21, p5-Class-Load-XS-0.08, p5-Clone-0.35, p5-Convert-BinHex-1.123, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.72, p5-DBD-mysql-4.028, p5-DBI-1.631, p5-Data-OptList-0.109, p5-Data-Stag-0.14_1, p5-Devel-GlobalDestruction-0.13, p5-Devel-StackTrace-1.34, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.9, p5-Dist-CheckConflicts-0.11, p5-Email-Date-Format-1.004, p5-Encode-Locale-1.03, p5-Error-0.17022, p5-Eval-Closure-0.11, p5-Exception-Class-1.38, p5-File-Listing-6.04, p5-File-Slurp-Tiny-0.003, p5-File-Temp-0.23.04, p5-GD-2.53, p5-GD-SVG-0.33_5, p5-Graph-0.96,1, p5-GraphViz-2.15, p5-HTML-Element-Extended-1.18, p5-HTML-Parser-3.71, p5-HTML-TableExtract-2.11, p5-HTML-Tagset-3.20, p5-HTML-Tree-5.03, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-Hash-AutoHash-1.17, p5-Hash-AutoHash-Args-1.18, p5-Heap-0.80, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-IO-String-1.08, p5-IO-Tty-1.12, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.06, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.03.0, p5-MIME-Tools-5.505,2, p5-MIME-Types-2.08, p5-MRO-Compat-0.12, p5-Mail-Tools-2.13, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.02, p5-Module-Build-0.4206, p5-Module-Implementation-0.09, p5-Module-Runtime-0.014, p5-Moose-2.1204,1, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.36, p5-Package-Stash-XS-0.28, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-Path-Class-0.34, p5-PathTools-3.4700, p5-PostScript-0.06, p5-SOAP-Lite-0.716, p5-SVG-2.59, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.35,1, p5-Set-Scalar-1.26, p5-Socket-2.015, p5-Sort-Naturally-1.03, p5-Spreadsheet-ParseExcel-0.65,1, p5-Statistics-Descriptive-3.0605, p5-Sub-Exporter-0.987, p5-Sub-Exporter-Progressive-0.001.011, p5-Sub-Install-0.928, p5-Sub-Name-0.05, p5-Sub-Uplevel-0.2400, p5-Task-Weaken-1.04, p5-Test-Deep-0.113, p5-Test-Differences-0.620,1, p5-Test-Exception-0.32, p5-Test-Most-0.33, p5-Test-NoWarnings-1.04_1, p5-Test-Tester-0.10.9, p5-Test-Warn-0.30, p5-Text-Diff-1.41, p5-Text-Iconv-1.7_1, p5-Text-Shellwords-1.08, p5-Text-Tabs+Wrap-2013.0523, p5-Tie-IxHash-1.23, p5-Tie-ToObject-0.03_1, p5-TimeDate-2.30_1,1, p5-Tree-DAG_Node-1.22, p5-Try-Tiny-0.18, p5-URI-1.64, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41_1, p5-XML-RegExp-0.04, p5-XML-SAX-0.99_1, p5-XML-SAX-Base-1.08, p5-XML-SAX-Expat-0.51, p5-XML-SAX-Writer-0.54, p5-XML-Simple-2.20, p5-XML-Twig-3.48, p5-XML-Writer-0.625, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.14, p5-YAML-1.11, p5-libwww-6.08, p5-libxml-0.08, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, printproto-1.0.5, python27-2.7.8_5, renderproto-0.11.1, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xorg-fonts-truetype-7.7_1, xproto-7.0.26
Also listed in: Perl5

p5-bioperl-run-1.6.901
Wrapper modules for common bioinformatics tools
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: cairo-1.12.16_1,2, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, graphviz-2.38.0_1, harfbuzz-0.9.28, icu-53.1, indexinfo-0.2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXft-2.3.1_2, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libgd-2.1.0_4,1, libiconv-1.14_4, libltdl-2.4.2_3, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mysql55-client-5.5.39, p5-Algorithm-C3-0.10, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-2.02, p5-Authen-NTLM-1.09, p5-Bio-ASN1-EntrezGene-1.091, p5-Carp-1.33.01, p5-Class-AutoClass-1.56, p5-Class-C3-0.27, p5-Class-Data-Inheritable-0.08, p5-Class-Inspector-1.28, p5-Class-Load-0.21, p5-Class-Load-XS-0.08, p5-Clone-0.35, p5-Config-Any-0.24, p5-Config-General-2.56, p5-Config-Tiny-2.20, p5-Convert-BinHex-1.123, p5-Convert-Binary-C-0.76, p5-Crypt-RC4-2.02, p5-Crypt-SSLeay-0.72, p5-DBD-mysql-4.028, p5-DBI-1.631, p5-Data-OptList-0.109, p5-Data-Stag-0.14_1, p5-Devel-GlobalDestruction-0.13, p5-Devel-StackTrace-1.34, p5-Digest-HMAC-1.03, p5-Digest-Perl-MD5-1.9, p5-Dist-CheckConflicts-0.11, p5-Email-Date-Format-1.004, p5-Encode-Locale-1.03, p5-Error-0.17022, p5-Eval-Closure-0.11, p5-Exception-Class-1.38, p5-File-Listing-6.04, p5-File-Slurp-Tiny-0.003, p5-File-Sort-1.01, p5-File-Temp-0.23.04, p5-Filter-1.50, p5-GD-2.53, p5-GD-SVG-0.33_5, p5-Graph-0.96,1, p5-GraphViz-2.15, p5-HTML-Element-Extended-1.18, p5-HTML-Parser-3.71, p5-HTML-TableExtract-2.11, p5-HTML-Tagset-3.20, p5-HTML-Tree-5.03, p5-HTTP-Cookies-6.01, p5-HTTP-Daemon-6.01, p5-HTTP-Date-6.02, p5-HTTP-Message-6.06_2, p5-HTTP-Negotiate-6.01, p5-Hash-AutoHash-1.17, p5-Hash-AutoHash-Args-1.18, p5-Heap-0.80, p5-IO-HTML-1.001, p5-IO-Socket-IP-0.32, p5-IO-Socket-SSL-1.998, p5-IO-String-1.08, p5-IO-Tty-1.12, p5-IO-stringy-2.110, p5-IPC-Run-0.92, p5-JSON-XS-3.01, p5-LWP-MediaTypes-6.02, p5-LWP-Protocol-https-6.06, p5-List-MoreUtils-0.33, p5-MIME-Lite-3.03.0, p5-MIME-Tools-5.505,2, p5-MIME-Types-2.08, p5-MRO-Compat-0.12, p5-Mail-Tools-2.13, p5-Math-Derivative-0.01, p5-Math-Random-0.71, p5-Math-Spline-0.02, p5-Module-Build-0.4206, p5-Module-Implementation-0.09, p5-Module-Runtime-0.014, p5-Moose-2.1204,1, p5-Mozilla-CA-20130114, p5-Net-HTTP-6.07, p5-Net-SSLeay-1.66, p5-OLE-Storage_Lite-0.19, p5-Package-DeprecationManager-0.13, p5-Package-Stash-0.36, p5-Package-Stash-XS-0.28, p5-Params-Util-1.07, p5-Parse-RecDescent-1.967.009_1, p5-Path-Class-0.34, p5-PathTools-3.4700, p5-PostScript-0.06, p5-SOAP-Lite-0.716, p5-SVG-2.59, p5-SVG-Graph-0.04, p5-Scalar-List-Utils-1.35,1, p5-Set-Scalar-1.26, p5-Socket-2.015, p5-Sort-Naturally-1.03, p5-Spreadsheet-ParseExcel-0.65,1, p5-Statistics-Descriptive-3.0605, p5-Sub-Exporter-0.987, p5-Sub-Exporter-Progressive-0.001.011, p5-Sub-Install-0.928, p5-Sub-Name-0.05, p5-Sub-Uplevel-0.2400, p5-Task-Weaken-1.04, p5-Test-Deep-0.113, p5-Test-Differences-0.620,1, p5-Test-Exception-0.32, p5-Test-Most-0.33, p5-Test-NoWarnings-1.04_1, p5-Test-Tester-0.10.9, p5-Test-Warn-0.30, p5-Text-Diff-1.41, p5-Text-Iconv-1.7_1, p5-Text-Shellwords-1.08, p5-Text-Tabs+Wrap-2013.0523, p5-Tie-IxHash-1.23, p5-Tie-ToObject-0.03_1, p5-TimeDate-2.30_1,1, p5-Tree-DAG_Node-1.22, p5-Try-Tiny-0.18, p5-Types-Serialiser-1.0, p5-URI-1.64, p5-WWW-RobotRules-6.02, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-NamespaceSupport-1.11, p5-XML-Parser-2.41_1, p5-XML-RegExp-0.04, p5-XML-SAX-0.99_1, p5-XML-SAX-Base-1.08, p5-XML-SAX-Expat-0.51, p5-XML-SAX-Writer-0.54, p5-XML-Simple-2.20, p5-XML-Twig-3.48, p5-XML-Writer-0.625, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.14, p5-YAML-1.11, p5-YAML-LibYAML-0.52, p5-bioperl-1.6.924, p5-common-sense-3.6, p5-libwww-6.08, p5-libxml-0.08, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, printproto-1.0.5, python27-2.7.8_5, renderproto-0.11.1, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xorg-fonts-truetype-7.7_1, xproto-7.0.26
Also listed in: Perl5

paml-4.8
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_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-3.695_3
Phylogeny Inference Package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-4.3.24, gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXaw-1.0.12_2,2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXmu-1.1.2_2,1, libXp-1.0.2_2,1, libXpm-3.5.11_2, libXt-1.1.4_2,1, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, printproto-1.0.5, xextproto-7.3.0, xproto-7.0.26

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-1.14, automake-wrapper-20131203, indexinfo-0.2, m4-1.4.17_1,1, perl5-5.16.3_11

platon-2014.07.13_1
Tool for viewing molecular/crystallographic structures
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.24_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, kbproto-1.0.6, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, xproto-7.0.26

plink-1.07_4
Whole genome association analysis toolset
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: binutils-2.24_1, blas-3.4.2_3, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmake-3.82_1, gmp-5.1.3_2, indexinfo-0.2, lapack-3.4.2_3, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2
Also listed in: Science

plinkseq-0.08_2
Toolset for working with human genetic variation data
Long description | Changes | Main Web Site
Maintained by: jwbacon@tds.net
Requires: protobuf-2.5.0_4
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_5, kbproto-1.0.6, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, png-1.5.18, povray-meta-0.1, povray36-3.6.1_12, svgalib-1.4.3_7, tiff-4.0.3_4, xproto-7.0.26
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-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4

protomol-2.0.3_10
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.24_1, damageproto-1.2.1, dri2proto-2.8, expat-2.1.0_1, fixesproto-5.0, freeglut-2.8.1_3, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, inputproto-2.3.1, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXi-1.7.4,1, libXmu-1.1.2_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libglapi-9.1.7_1, libiconv-1.14_4, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mpc-1.0.2_1, mpfr-3.1.2_2, pciids-20140916, png-1.5.18, randrproto-1.4.0, renderproto-0.11.1, tiff-4.0.3_4, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.26

psi88-1.0_7
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.24_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2

py27-biopython-1.60_4
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: binutils-2.24_1, blas-3.4.2_3, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, lapack-3.4.2_3, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2, py27-nose-1.3.3, py27-numpy-1.8.1_3,1, py27-reportlab1-1.21.2_3, py27-setuptools27-5.5.1, python2-2_3, python27-2.7.8_5, 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-2.24_1, blas-3.4.2_3, cython-0.20.2, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, lapack-3.4.2_3, libiconv-1.14_4, libxml2-2.9.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, mysql55-client-5.5.39, postgresql92-client-9.2.9, py27-Babel-1.3_2, py27-Jinja2-2.7.3, py27-MarkupSafe-0.23, py27-MySQLdb-1.2.3_4, py27-docutils-0.12, py27-nose-1.3.3, py27-numpy-1.8.1_3,1, py27-psycopg2-2.5.3, py27-pygments-1.6_2, py27-pytz-2014.4,1, py27-setuptools27-5.5.1, py27-sphinx-1.2.3, py27-sqlalchemy06-0.6.9_1, py27-sqlite3-2.7.8_5, python2-2_3, python27-2.7.8_5, sqlite3-3.8.6, 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-2.24_1, blas-3.4.2_3, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, lapack-3.4.2_3, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2, py27-nose-1.3.3, py27-numpy-1.8.1_3,1, py27-setuptools27-5.5.1, python27-2.7.8_5, 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-0.18.3.1_1, indexinfo-0.2, libiconv-1.14_4, py27-setuptools27-5.5.1, python27-2.7.8_5
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-6.8.9.4_4,1, atk-2.8.0_1, binutils-2.24_1, cairo-1.12.16_1,2, compositeproto-0.4.2, cups-client-1.7.3_2, cups-image-1.7.3_1, damageproto-1.2.1, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, fftw3-3.3.3_2, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, ghostscript9-9.06_8, giflib-nox11-4.2.3_3, glib-2.36.3_4, gmp-5.1.3_2, gnomehier-3.0, graphite2-1.2.4, gsfonts-8.11_6, gtk-engines2-2.20.2_2, gtk-update-icon-cache-2.24.22, gtk2-2.24.22_4, harfbuzz-0.9.28, hicolor-icon-theme-0.12, icu-53.1, indexinfo-0.2, inputproto-2.3.1, jasper-1.900.1_14, jbig2dec-0.11_2, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, lcms2-2.6_3, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libcroco-0.6.8_2, libffi-3.0.13_2, libfontenc-1.1.2_2, libfpx-1.3.1.4, libgd-2.1.0_4,1, libgsf-1.14.28_2, libiconv-1.14_4, libidn-1.28_2, liblqr-1-0.4.1_8, libltdl-2.4.2_3, libpaper-1.1.24.3, libpthread-stubs-0.3_6, librsvg2-2.36.4_2, libwmf-0.2.8.4_12, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, openjpeg-2.1.0, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, python-2.7_2,2, python2-2_3, python27-2.7.8_5, randrproto-1.4.0, renderproto-0.11.1, shared-mime-info-1.1_1, svgalib-1.4.3_7, tiff-4.0.3_4, webp-0.4.1, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26
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

ruby19-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, libexecinfo-1.1_3, libffi-3.0.13_2, libyaml-0.1.6_1, readline-6.3.8, ruby-1.9.3.547_3,1
Also listed in: Ruby

seaview-4.5.2_1
Multiple DNA/protein sequence alignment editor
Long description | Changes | Main Web Site
Maintained by: 5u623l20@gmail.com
Requires: binutils-2.24_1, damageproto-1.2.1, dri2proto-2.8, expat-2.1.0_1, fixesproto-5.0, fltk-1.3.2_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmake-3.82_1, gmp-5.1.3_2, indexinfo-0.2, jpeg-8_5, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXinerama-1.1.3_2,1, libXrender-0.9.8_2, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libglapi-9.1.7_1, libiconv-1.14_4, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mpc-1.0.2_1, mpfr-3.1.2_2, pciids-20140916, pdflib-7.0.5_3, png-1.5.18, renderproto-0.11.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.26

seqan-1.3.1_3
C++ Sequence Analysis Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: binutils-2.24_1, ca_root_nss-3.17, cmake-3.0.2, cmake-modules-3.0.2, curl-7.38.0_1, expat-2.1.0_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2, python27-2.7.8_5

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-4.28
Tools for visualising sequence alignments
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: atk-2.8.0_1, ca_root_nss-3.17, cairo-1.12.16_1,2, compositeproto-0.4.2, cups-client-1.7.3_2, curl-7.38.0_1, damageproto-1.2.1, dejavu-2.34_4, encodings-1.0.4_1,1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, glib-2.36.3_4, gnomehier-3.0, graphite2-1.2.4, gtk-update-icon-cache-2.24.22, gtk2-2.24.22_4, harfbuzz-0.9.28, hicolor-icon-theme-0.12, icu-53.1, indexinfo-0.2, inputproto-2.3.1, intltool-0.50.2, jasper-1.900.1_14, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libexecinfo-1.1_3, libffi-3.0.13_2, libfontenc-1.1.2_2, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, mkfontdir-1.0.7, mkfontscale-1.1.1_1, p5-XML-Parser-2.41_1, pango-1.34.1_7, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, pkgconf-0.9.6_1, png-1.5.18, python-2.7_2,2, python2-2_3, python27-2.7.8_5, randrproto-1.4.0, renderproto-0.11.1, shared-mime-info-1.1_1, sqlite3-3.8.6, tiff-4.0.3_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26

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: gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4

tRNAscan-SE-1.23_1
Improved tool for transfer RNA detection
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.16.3_11

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-2.24_1, clustalw-2.1_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, libiconv-1.14_4, mpc-1.0.2_1, mpfr-3.1.2_2

tinker-6.2.6_6
General purpose molecular modelling package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.24_1, gcc-4.8.3_1, gcc-ecj-4.5, gettext-0.18.3.1_1, gmp-5.1.3_2, indexinfo-0.2, libiconv-1.14_4, mpc-1.0.2_1, 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-2.8.0_1, binutils-2.24_1, cairo-1.12.16_1,2, compositeproto-0.4.2, cups-client-1.7.3_2, damageproto-1.2.1, dbus-1.8.8, dbus-glib-0.100.2_1, dconf-0.14.1_1, dejavu-2.34_4, dri2proto-2.8, encodings-1.0.4_1,1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gconf2-2.32.0_6, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, glib-2.36.3_4, gmake-3.82_1, gmp-5.1.3_2, gnome_subr-1.0, gnomehier-3.0, gobject-introspection-1.36.0_3, graphite2-1.2.4, gstreamer-0.10.36_2, gstreamer-plugins-0.10.36_4,3, gtk-update-icon-cache-2.24.22, gtk2-2.24.22_4, harfbuzz-0.9.28, hicolor-icon-theme-0.12, icu-53.1, indexinfo-0.2, inputproto-2.3.1, jasper-1.900.1_14, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, libGL-9.1.7_2, libGLU-9.0.0_2, libICE-1.0.9,1, libIDL-0.8.14_2, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXv-1.0.10_2,1, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libffi-3.0.13_2, libfontenc-1.1.2_2, libglapi-9.1.7_1, libiconv-1.14_4, libmspack-0.4_2, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, orc-0.4.21, pango-1.34.1_7, pangox-compat-0.0.2_1, pciids-20140916, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, polkit-0.105_3, python-2.7_2,2, python2-2_3, python27-2.7.8_5, randrproto-1.4.0, renderproto-0.11.1, shared-mime-info-1.1_1, tiff-4.0.3_4, videoproto-2.3.2, wx28-gtk2-common-2.8.12_4, wx28-gtk2-contrib-common-2.8.12_4, wx28-gtk2-unicode-2.8.12_4, wx28-gtk2-unicode-contrib-2.8.12_4, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.26

ugene-1.14.0_1
Free, open-source, cross-platform bioinformatics toolkit
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: atk-2.8.0_1, bash-4.3.24, binutils-2.24_1, ca_root_nss-3.17, cairo-1.12.16_1,2, compositeproto-0.4.2, damageproto-1.2.1, dejavu-2.34_4, dri2proto-2.8, encodings-1.0.4_1,1, expat-2.1.0_1, fixesproto-5.0, font-bh-ttf-1.0.3_1, font-misc-ethiopic-1.0.3_1, font-misc-meltho-1.0.3_1, font-util-1.3.0_1, fontcacheproto-0.1.3, fontconfig-2.11.0_3,1, freetype2-2.5.3_2, gcc-4.8.3_1, gcc-ecj-4.5, gdk-pixbuf2-2.28.2_1, gettext-0.18.3.1_1, glib-2.36.3_4, glproto-1.4.17, gmp-5.1.3_2, gnomehier-3.0, gobject-introspection-1.36.0_3, graphite2-1.2.4, gstreamer-0.10.36_2, gstreamer-plugins-0.10.36_4,3, gtk-update-icon-cache-2.24.22, harfbuzz-0.9.28, hicolor-icon-theme-0.12, icu-53.1, indexinfo-0.2, inputproto-2.3.1, jasper-1.900.1_14, jbigkit-2.1_1, jpeg-8_5, kbproto-1.0.6, lcms-1.19_5,1, libGL-9.1.7_2, libGLU-9.0.0_2, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXcomposite-0.4.4_2,1, libXcursor-1.1.14_2, libXdamage-1.1.4_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXfontcache-1.0.5_2, libXft-2.3.1_2, libXi-1.7.4,1, libXinerama-1.1.3_2,1, libXmu-1.1.2_2,1, libXrandr-1.4.2_2, libXrender-0.9.8_2, libXt-1.1.4_2,1, libXtst-1.2.2_2, libXv-1.0.10_2,1, libXxf86vm-1.1.3_2, libdrm-2.4.52_1,1, libexecinfo-1.1_3, libffi-3.0.13_2, libfontenc-1.1.2_2, libglapi-9.1.7_1, libiconv-1.14_4, libmng-1.0.10_2, libpciaccess-0.13.2_2, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, libxshmfence-1.1_3, mkfontdir-1.0.7, mkfontscale-1.1.1_1, mpc-1.0.2_1, mpfr-3.1.2_2, orc-0.4.21, pango-1.34.1_7, pciids-20140916, pcre-8.35, perl5-5.16.3_11, pixman-0.32.4_3, png-1.5.18, python2-2_3, python27-2.7.8_5, qt4-assistant-4.8.6_1, qt4-clucene-4.8.6_1, qt4-corelib-4.8.6_3, qt4-declarative-4.8.6_2, qt4-doc-4.8.6, qt4-gui-4.8.6_2, qt4-help-4.8.6_1, qt4-imageformats-4.8.6_1, qt4-linguist-4.8.6_1, 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-sqlite-plugin-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-1.4.0, recordproto-1.14.2, renderproto-0.11.1, shared-mime-info-1.1_1, sqlite3-3.8.6, tiff-4.0.3_4, videoproto-2.3.2, xcb-util-0.3.9_3,1, xcb-util-renderutil-0.3.9, 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-7.0.26, xset-1.2.3_1
Also listed in: Science

velvet-1.2.10_1
Sequence assembler for very short reads
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-0.18.3.1_1, gmake-3.82_1, indexinfo-0.2, libiconv-1.14_4, perl5-5.16.3_11, python27-2.7.8_5

wise-2.4.1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.18.3.1_1, glib-2.36.3_4, indexinfo-0.2, libffi-3.0.13_2, libiconv-1.14_4, pcre-8.35, perl5-5.16.3_11, pkgconf-0.9.6_1, python27-2.7.8_5

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-0.18.3.1_1, glib12-1.2.10_15, gmake-3.82_1, gtk12-1.2.10_24, indexinfo-0.2, inputproto-2.3.1, kbproto-1.0.6, libICE-1.0.9,1, libSM-1.2.2_2,1, libX11-1.6.2_2,1, libXau-1.0.8_2, libXdmcp-1.1.1_2, libXext-1.3.2_2,1, libXfixes-5.0.1_2, libXi-1.7.4,1, libiconv-1.14_4, libpthread-stubs-0.3_6, libxcb-1.10_2, libxml2-2.9.1_1, xextproto-7.3.0, xproto-7.0.26

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