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FreeBSD Ports: Biology

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Software related to biology.

InsightToolkit-2.8.1_2
Insight Toolkit
Long description | Sources | Main Web Site
Maintained by: jwbacon@tds.net
Requires: cmake-2.6.3_1
Also listed in: Science

LBreeder-1.0_12
Allows you to display and breed L-system forms
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-1.26.0, bitstream-vera-1.10_4, cairo-1.8.8,1, compositeproto-0.4, damageproto-1.1.0_2, dri2proto-2.0, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gmake-3.81_3, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXmu-1.0.4,1, libXrandr-1.3.0, libXrender-0.9.4_1, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libfontenc-1.0.4, libglut-7.4.4, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, python25-2.5.4_1, randrproto-1.3.0, renderproto-0.9.3, shared-mime-info-0.60_1, tiff-3.8.2_3, wxgtk2-2.4.2_16, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15

adun-0.8.2_2
Molecular Simulator for GNUstep
Long description | Sources | Main Web Site
Maintained by: dinoex@FreeBSD.org
Requires: aspell-0.60.6_2, cups-client-1.3.10_2, expat-2.0.1, ffcall-1.10_1, fontconfig-2.6.0,1, freetype-1.3.1_4, freetype2-2.3.9_1, gcc-4.2.5.20090325, gettext-0.17_1, gmake-3.81_3, gnustep-back-0.16.0, gnustep-base-1.18.0, gnustep-gui-0.16.0, gnustep-make-2.2.0, gnutls-2.6.5, gsl-1.12, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXft-2.1.13, libXmu-1.0.4,1, libXrender-0.9.4_1, libXt-1.0.5_1, libaudiofile-0.2.6, libgcrypt-1.4.4, libgmp-4.3.1, libgpg-error-1.7, libiconv-1.13, libpthread-stubs-0.1, libungif-4.1.4_5, libxcb-1.3, libxml2-2.7.3, libxslt-1.1.24_2, mpfr-2.4.1_1, pkg-config-0.23_1, png-1.2.35, portaudio-19.20071207, python25-2.5.4_1, renderproto-0.9.3, tiff-3.8.2_3, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Gnustep

afni-2008.01.02.1043_2
Advanced Functional Neuro Imaging
Long description | Package | Sources | Main Web Site
Maintained by: jwbacon@tds.net
Requires: damageproto-1.1.0_2, dri2proto-2.0, endian-1.0, expat-2.0.1, fixesproto-4.0, gettext-0.17_1, gmake-3.81_3, inputproto-1.5.0, jbigkit-1.6, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libGLw-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXi-1.2.1,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, mpeg_encode-1.5b, netpbm-10.26.63, open-motif-2.2.3_6, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, tiff-3.8.2_3, whirlgif-3.04, xbitmaps-1.0.1, xcb-proto-1.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xproto-7.0.15
Also listed in: Science, Graphics

ariadne-1.3
Programs to compare protein sequences and profiles
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

artemis-9_1
A DNA sequence viewer and annotation tool
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: diablo-jdk-1.6.0.07.02_5, inputproto-1.5.0, javavmwrapper-2.3.3, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXi-1.2.1,1, libXp-1.0.0,1, libXt-1.0.5_1, libXtst-1.0.3_1, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, recordproto-1.13.2, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Java

avida-2.8.1_1
Avida is an auto-adaptive genetic system designed for ALife research
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: cmake-2.6.3_1, gcc-4.2.5.20090325, libgmp-4.3.1, libiconv-1.13, mpfr-2.4.1_1

babel-1.6_3
Converts among various molecular file formats
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Also listed in: Converters

belvu-2.29
A viewer for multiple sequence alignments
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: linux_base-fc-4_14

biococoa-1.6.0_2
Bioinformatics framework
Long description | Sources | Main Web Site
Maintained by: dinoex@FreeBSD.org
Requires: aspell-0.60.6_2, cups-client-1.3.10_2, expat-2.0.1, ffcall-1.10_1, fontconfig-2.6.0,1, freetype-1.3.1_4, freetype2-2.3.9_1, gcc-4.2.5.20090325, gettext-0.17_1, gmake-3.81_3, gnustep-back-0.16.0, gnustep-base-1.18.0, gnustep-gui-0.16.0, gnustep-make-2.2.0, gnutls-2.6.5, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXft-2.1.13, libXmu-1.0.4,1, libXrender-0.9.4_1, libXt-1.0.5_1, libaudiofile-0.2.6, libgcrypt-1.4.4, libgmp-4.3.1, libgpg-error-1.7, libiconv-1.13, libpthread-stubs-0.1, libungif-4.1.4_5, libxcb-1.3, libxml2-2.7.3, libxslt-1.1.24_2, mpfr-2.4.1_1, pkg-config-0.23_1, png-1.2.35, portaudio-19.20071207, python25-2.5.4_1, renderproto-0.9.3, tiff-3.8.2_3, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Gnustep

biojava-1.7,1
Open-source java tools for processing biological data
Long description | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: apache-ant-1.7.1, diablo-jdk-1.6.0.07.02_5, inputproto-1.5.0, javavmwrapper-2.3.3, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXi-1.2.1,1, libXp-1.0.0,1, libXt-1.0.5_1, libXtst-1.0.3_1, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, recordproto-1.13.2, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Java

blat-34
A fast tool for local sequence similarity searches
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

boinc-simap-5.10.5.09_2
Similarity Matrix of Proteins project for BOINC
Long description | Package | Sources | Main Web Site
Maintained by: pav@FreeBSD.org
Requires: ORBit2-2.14.17, atk-1.26.0, bitstream-vera-1.10_4, boinc-client-6.4.5_3, ca_root_nss-3.11.9_2, cairo-1.8.8,1, compositeproto-0.4, curl-7.19.5_1, damageproto-1.1.0_2, dbus-1.2.4.6, dbus-glib-0.80, dri2proto-2.0, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gconf2-2.26.2, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gnome_subr-1.0, gnomehier-2.3_12, gstreamer-0.10.23, gstreamer-plugins-0.10.23,3, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libIDL-0.8.13, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXmu-1.0.4,1, libXrandr-1.3.0, libXrender-0.9.4_1, libXt-1.0.5_1, libXv-1.0.4,1, libXxf86vm-1.0.2, libdrm-2.4.11, libfontenc-1.0.4, libglut-7.4.4, libiconv-1.13, libmspack-0.0.20060920, liboil-0.3.16, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, policykit-0.9_4, popt-1.14, python25-2.5.4_1, randrproto-1.3.0, renderproto-0.9.3, shared-mime-info-0.60_1, tiff-3.8.2_3, videoproto-2.2.2, wxgtk2-2.8.10, wxgtk2-common-2.8.10, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15

chemeq-1.50_1
Outputs LaTeX code for chemical reaction
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bison-2.4.1,1, gettext-0.17_1, libiconv-1.13, m4-1.4.13,1
Also listed in: Textproc

clustalw-2.0.6
A multiple alignment program for DNA or proteins
Long description | Sources | Main Web Site
Maintained by: wenheping@gmail.com

consed-16.0
A graphical tool for editing Phrap assemblies
Long description | Sources | Main Web Site
Maintained by: mzaki@biol.s.u-tokyo.ac.jp
Requires: linux-expat-1.95.8_2, linux-fontconfig-2.2.3_9, linux-xorg-libs-6.8.2_7, linux_base-fc-4_14, perl-5.8.9_3, phd2fasta-0.990622.f, phrap-0.990329, phred-0.020425.c

crimap-2.4
Creation of multilocus linkage maps
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

crux-1.1.0
Software toolkit for phylogenetic inference
Long description | Sources | Main Web Site
Maintained by: jasone@FreeBSD.org
Requires: gcc-4.3.4.20090621, gettext-0.17_1, gmake-3.81_3, libgmp-4.3.1, libiconv-1.13, mpfr-2.4.1_1, python25-2.5.4_1
Also listed in: Python

cycle-0.3.1_3
A calendar program for women
Long description | Package | Sources | Main Web Site
Maintained by: danfe@FreeBSD.org
Requires: atk-1.26.0, bitstream-vera-1.10_4, cairo-1.8.8,1, compositeproto-0.4, damageproto-1.1.0_2, dri2proto-2.0, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXmu-1.0.4,1, libXrandr-1.3.0, libXrender-0.9.4_1, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libfontenc-1.0.4, libglut-7.4.4, libiconv-1.13, libmspack-0.0.20060920, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, py25-imaging-1.1.6_2, py25-numeric-24.2_3, py25-opengl-3.0.0, py25-tkinter-2.5.4_3, py25-wxPython-2.6.3.3_1, py25-wxPython-common-2.6.3.3_2, python25-2.5.4_1, randrproto-1.3.0, renderproto-0.9.3, shared-mime-info-0.60_1, tcl-8.5.7_1, tcl-modules-8.5.7, tiff-3.8.2_3, tk-8.5.7, wxgtk2-2.6.4, wxgtk2-common-2.6.4, wxgtk2-contrib-2.6.4, wxgtk2-contrib-common-2.6.4, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15
Also listed in: Deskutils, Python

distribfold-0.1.20040613
distributedfolding.org distributed protein folding project
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: compat4x-i386-5.3_9, localedata-5.4
Also listed in: Net

dna-qc-1993.07.26
A quality control algorithm for DNA sequencing projects
Long description | Package | Sources
Maintained by: ports@FreeBSD.org

dotter-20021204
A viewer for multiple sequence alignments
Long description | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: linux_base-fc-4_14

dtiquery-1.1_1
Stanford DTI Visualization tool
Long description | Sources | Main Web Site
Maintained by: jwbacon@tds.net
Requires: ORBit2-2.14.17, atk-1.26.0, bitstream-vera-1.10_4, cairo-1.8.8,1, compositeproto-0.4, cups-client-1.3.10_2, damageproto-1.1.0_2, dbus-1.2.4.6, dbus-glib-0.80, dri2proto-2.0, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gconf2-2.26.2, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gmake-3.81_3, gnome_subr-1.0, gnomehier-2.3_12, gnutls-2.6.5, gstreamer-0.10.23, gstreamer-plugins-0.10.23,3, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, jama-1.2.5, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, lcms-1.18a,1, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libIDL-0.8.13, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXrandr-1.3.0, libXrender-0.9.4_1, libXt-1.0.5_1, libXv-1.0.4,1, libXxf86vm-1.0.2, libdrm-2.4.11, libfontenc-1.0.4, libgcrypt-1.4.4, libgpg-error-1.7, libiconv-1.13, libmng-1.0.10, libmspack-0.0.20060920, liboil-0.3.16, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, nas-1.9.1_3, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, policykit-0.9_4, popt-1.14, printproto-1.0.4, python25-2.5.4_1, qt-3.3.8_9, randrproto-1.3.0, rapid-2.01, renderproto-0.9.3, shared-mime-info-0.60_1, tcl-8.4.19_3,1, tiff-3.8.2_3, tk-8.4.19_2,2, tnt-1.2.6, videoproto-2.2.2, vtk-5.0.4_3, wxgtk2-2.8.10, wxgtk2-common-2.8.10, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15
Also listed in: Science

embassy-6.0.0
A collection of contributed EMBOSS applications
Long description | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: emboss-6.0.1, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, gmake-3.81_3, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, open-motif-2.2.3_6, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, xbitmaps-1.0.1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

emboss-6.0.1
A collection of open source tools for genetic sequence analysis
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: clustalw-2.0.6, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, gmake-3.81_3, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libpthread-stubs-0.1, libtool-1.5.26, libxcb-1.3, open-motif-2.2.3_6, pkg-config-0.23_1, png-1.2.35, primer3-1.1.3, printproto-1.0.4, python25-2.5.4_1, xbitmaps-1.0.1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

fasta-21.u1.d1
A collection of programs for searching DNA and protein databases
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

fasta3-35.4.7
A collection of programs for searching DNA and protein databases
Long description | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar

fastdnaml-1.2.2_1
Faster DNAML, makes phylogenetic trees using maximum likelihood
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

finchtv-1.3.1
A chromatogram trace viewer
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: linux_base-fc-4_14

fluctuate-1.40
A program to fit population models
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

garlic-1.5_2
Molecular viewer, editor and visualization program
Long description | Package | Sources | Main Web Site
Maintained by: maho@FreeBSD.org
Requires: gettext-0.17_1, gmake-3.81_3, kbproto-1.0.3, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, python25-2.5.4_1, xcb-proto-1.5, xproto-7.0.15

genpak-0.26_4
A set of small utilities to manipulate DNA sequences
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, gmake-3.81_3, jpeg-6b_7, libiconv-1.13, pkg-config-0.23_1, png-1.2.35

gff2ps-0.98d_2
Converts gff-formated genomic data-sets to PostScript
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-4.0.24, gawk-3.1.6_1, gettext-0.17_1, libiconv-1.13

gmap-2006.04.21
A Genomic Mapping and Alignment Program for mRNA and EST Sequences
Long description | Package | Sources | Main Web Site
Maintained by: rpz@cse.wustl.edu
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

gperiodic-2.0.10_2
Displays a periodic table of the elements
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-1.26.0, bitstream-vera-1.10_4, cairo-1.8.8,1, compositeproto-0.4, damageproto-1.1.0_2, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, intltool-0.40.6, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, libX11-1.2.1_1,1, libXau-1.0.4, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXrandr-1.3.0, libXrender-0.9.4_1, libfontenc-1.0.4, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, p5-XML-Parser-2.36, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, python25-2.5.4_1, randrproto-1.3.0, renderproto-0.9.3, shared-mime-info-0.60_1, tiff-3.8.2_3, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

hmmer-2.3.2
Profile hidden Markov models for biological sequence analysis
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: perl-5.8.9_3

jalview-2.07_2
A viewer and editor for multiple sequence alignments
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: apache-ant-1.7.1, diablo-jdk-1.6.0.07.02_5, inputproto-1.5.0, javavmwrapper-2.3.3, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXi-1.2.1,1, libXp-1.0.0,1, libXt-1.0.5_1, libXtst-1.0.3_1, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, recordproto-1.13.2, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Java

kinemage-5.79_1
A molecular visualization program with special functions
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libpthread-stubs-0.1, libxcb-1.3, open-motif-2.2.3_6, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, xbitmaps-1.0.1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

lagan-1.2
Efficient tools for large-scale multiple alignments of genomic DNA
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: perl-5.8.9_3

lamarc-2.1.3,1
A package of programs for computing population parameters
Long description | Sources | Main Web Site
Maintained by: pgollucci@FreeBSD.org

libgenome-0.5.2_1
Toolkit for developing bioinformatic related software in C++
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: libtool-1.5.26

libsbml-3.3.2
An API Library for Working with SBML File
Long description | Package | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13, libxml2-2.7.3, pkg-config-0.23_1
Also listed in: Devel

linux-foldingathome-5.04
Distributed client for Protein Folding
Long description | Package | Sources | Main Web Site
Maintained by: onatan@gmail.com
Requires: linux_base-fc-4_14

lsysexp-0.67_8
A GTK based program for viewing and creating L-system fractals
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-1.26.0, bitstream-vera-1.10_4, cairo-1.8.8,1, compositeproto-0.4, damageproto-1.1.0_2, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, intltool-0.40.6, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, libX11-1.2.1_1,1, libXau-1.0.4, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXrandr-1.3.0, libXrender-0.9.4_1, libfontenc-1.0.4, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, p5-XML-Parser-2.36, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, python25-2.5.4_1, randrproto-1.3.0, renderproto-0.9.3, shared-mime-info-0.60_1, tiff-3.8.2_3, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15

mafft-5.743
Multiple sequence alignments based on fast Fourier transform
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: fasta3-35.4.7

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

migrate-3.0.3
A program to estimate population sizes and migration rates
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

minc-1.4_2
Medical Imaging NetCDF
Long description | Package | Sources | Main Web Site
Maintained by: jwbacon@tds.net
Requires: libtool-1.5.26, netcdf-3.6.3_3
Also listed in: Science

minc-2.0.09_1
Medical Imaging NetCDF
Long description | Package | Sources | Main Web Site
Maintained by: jwbacon@tds.net
Requires: hdf5-1.6.8_1, libtool-1.5.26, netcdf-3.6.3_3
Also listed in: Science

molden-4.6_1,1
Display molecular orbitals and electron densities in 2D and 3D
Long description | Sources | Main Web Site
Maintained by: oivulf@gmail.com
Requires: damageproto-1.1.0_2, dri2proto-2.0, expat-2.0.1, fixesproto-4.0, gcc-4.3.4.20090621, inputproto-1.5.0, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXi-1.2.1,1, libXmu-1.0.4,1, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libglut-7.4.4, libgmp-4.3.1, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, mpfr-2.4.1_1, pkg-config-0.23_1, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xproto-7.0.15

mopac-7.1.10_1,1
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: f2c-20060810_3, gettext-0.17_1, gmake-3.81_3, libiconv-1.13

mrbayes-3.1.2_1
Bayesian inference of phylogeny
Long description | Package | Sources | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13, readline-6.0_1

mummer-3.20
A modular system for rapid whole genome alignment
Long description | Package | Sources | Main Web Site
Maintained by: Anthony.Maher@uts.edu.au
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

muscle-3.6
MUltiple Sequence Comparison by Log-Expectation
Long description | Package | Sources | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

ncbi-toolkit-2009.03.01
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libpthread-stubs-0.1, libxcb-1.3, open-motif-2.2.3_6, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, xbitmaps-1.0.1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

njplot-2.1_1
Phylogenetic tree drawing program capable of interactive manipulation
Long description | Sources | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libpthread-stubs-0.1, libxcb-1.3, ncbi-toolkit-2009.03.01, open-motif-2.2.3_6, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, xbitmaps-1.0.1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

ortep3-1.0.3_4
The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.3.4.20090621, libgmp-4.3.1, libiconv-1.13, mpfr-2.4.1_1

p5-AcePerl-1.92
Perl5 interface to the ACEDB genome database system
Long description | Package | Sources | Main Web Site
Maintained by: pgollucci@FreeBSD.org
Requires: p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Digest-MD5-2.39, p5-Digest-SHA1-2.12, p5-Error-0.17015, p5-File-NFSLock-1.20, p5-Heap-0.80, p5-IO-String-1.08, p5-IPC-ShareLite-0.17, p5-Scalar-List-Utils-1.21,1, p5-TimeDate-1.16,1, perl-5.8.9_3
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.091
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: perl-5.8.9_3
Also listed in: Perl5

p5-Bio-Das-1.11
Client-side library for Distributed Genome Annotation System
Long description | Sources | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: expat-2.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, graphviz-2.22.2, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libltdl-1.5.26, libpthread-stubs-0.1, libxcb-1.3, mysql-client-5.0.83, p5-AcePerl-1.92, p5-Algorithm-Munkres-0.08, p5-Array-Compare-1.18, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Clone-0.31, p5-Compress-Raw-Zlib-2.020, p5-Compress-Zlib-2.015, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.74, p5-Crypt-SSLeay-0.57, p5-DBD-mysql-4.012, p5-DBI-1.60.7, p5-Data-Stag-0.11, p5-Digest-MD5-2.39, p5-Digest-SHA1-2.12, p5-Email-Date-Format-1.002, p5-Error-0.17015, p5-ExtUtils-CBuilder-0.24, p5-ExtUtils-ParseXS-2.19_1, p5-File-NFSLock-1.20, p5-File-Temp-0.22, p5-GD-2.43, p5-GD-SVG-0.33, p5-Graph-0.91,1, p5-GraphViz-2.04, p5-HTML-Parser-3.61, p5-HTML-Tagset-3.20, p5-HTML-Tree-3.23, p5-Heap-0.80, p5-IO-Compress-Base-2.015, p5-IO-Compress-Zlib-2.015, p5-IO-Socket-SSL-1.25, p5-IO-String-1.08, p5-IO-Tty-1.08, p5-IO-stringy-2.110, p5-IPC-Run-0.82, p5-IPC-ShareLite-0.17, p5-MIME-Base64-3.08, p5-MIME-Lite-3.02.4, p5-MIME-Tools-5.427_1,2, p5-MIME-Types-1.27, p5-Mail-Tools-2.04, p5-Math-Random-0.71, p5-Module-Build-0.33, p5-Net-SSLeay-1.35_1, p5-OLE-Storage_Lite-0.18, p5-Parse-RecDescent-1.96.0_2, p5-PostScript-0.06, p5-SOAP-Lite-0.710.08_1, p5-SVG-2.49, p5-SVG-Graph-0.02, p5-Scalar-List-Utils-1.21,1, p5-Set-Scalar-1.24, p5-Spreadsheet-ParseExcel-0.49,1, p5-Storable-2.20, p5-Test-Harness-3.17, p5-Text-Iconv-1.7, p5-Text-ParseWords-3.27, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-TimeDate-1.16,1, p5-URI-1.38, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.10, p5-XML-Parser-2.36, p5-XML-RegExp-0.03, p5-XML-SAX-0.96, p5-XML-SAX-Expat-0.40, p5-XML-SAX-Writer-0.52, p5-XML-Simple-2.18, p5-XML-Twig-3.32, p5-XML-Writer-0.606, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.12, p5-YAML-0.68, p5-bioperl-1.6.0, p5-libwww-5.828, p5-libxml-0.08, p5-version-0.76, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Perl5

p5-Bio-Glite-0.10
An Perl Interface to G-language
Long description | Package | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: p5-Compress-Raw-Zlib-2.020, p5-Compress-Zlib-2.015, p5-Data-Dumper-2.121, p5-HTML-Parser-3.61, p5-HTML-Tagset-3.20, p5-IO-Compress-Base-2.015, p5-IO-Compress-Zlib-2.015, p5-URI-1.38, p5-libwww-5.828, perl-5.8.9_3
Also listed in: Perl5

p5-Bio-Graphics-1.95
Generate GD Images of Bio::Seq Objects
Long description | Package | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: expat-2.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, graphviz-2.22.2, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libltdl-1.5.26, libpthread-stubs-0.1, libxcb-1.3, mysql-client-5.0.83, p5-AcePerl-1.92, p5-Algorithm-Munkres-0.08, p5-Array-Compare-1.18, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Clone-0.31, p5-Compress-Raw-Zlib-2.020, p5-Compress-Zlib-2.015, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.74, p5-Crypt-SSLeay-0.57, p5-DBD-mysql-4.012, p5-DBI-1.60.7, p5-Data-Stag-0.11, p5-Digest-MD5-2.39, p5-Digest-SHA1-2.12, p5-Email-Date-Format-1.002, p5-Error-0.17015, p5-ExtUtils-CBuilder-0.24, p5-ExtUtils-MakeMaker-6.52, p5-ExtUtils-ParseXS-2.19_1, p5-File-NFSLock-1.20, p5-File-Temp-0.22, p5-GD-2.43, p5-GD-SVG-0.33, p5-Graph-0.91,1, p5-GraphViz-2.04, p5-HTML-Parser-3.61, p5-HTML-Tagset-3.20, p5-HTML-Tree-3.23, p5-Heap-0.80, p5-IO-Compress-Base-2.015, p5-IO-Compress-Zlib-2.015, p5-IO-Socket-SSL-1.25, p5-IO-String-1.08, p5-IO-Tty-1.08, p5-IO-stringy-2.110, p5-IPC-Run-0.82, p5-IPC-ShareLite-0.17, p5-MIME-Base64-3.08, p5-MIME-Lite-3.02.4, p5-MIME-Tools-5.427_1,2, p5-MIME-Types-1.27, p5-Mail-Tools-2.04, p5-Math-Random-0.71, p5-Module-Build-0.33, p5-Net-SSLeay-1.35_1, p5-OLE-Storage_Lite-0.18, p5-Parse-RecDescent-1.96.0_2, p5-PostScript-0.06, p5-SOAP-Lite-0.710.08_1, p5-SVG-2.49, p5-SVG-Graph-0.02, p5-Scalar-List-Utils-1.21,1, p5-Set-Scalar-1.24, p5-Spreadsheet-ParseExcel-0.49,1, p5-Statistics-Descriptive-3.0000, p5-Storable-2.20, p5-Test-Harness-3.17, p5-Text-Iconv-1.7, p5-Text-ParseWords-3.27, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-TimeDate-1.16,1, p5-URI-1.38, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.10, p5-XML-Parser-2.36, p5-XML-RegExp-0.03, p5-XML-SAX-0.96, p5-XML-SAX-Expat-0.40, p5-XML-SAX-Writer-0.52, p5-XML-Simple-2.18, p5-XML-Twig-3.32, p5-XML-Writer-0.606, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.12, p5-YAML-0.68, p5-bioperl-1.6.0, p5-libwww-5.828, p5-libxml-0.08, p5-version-0.76, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Perl5

p5-Bio-MAGETAB-0.98
A data model and utility API for the MAGE-TAB format
Long description | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: p5-Algorithm-C3-0.08, p5-B-Hooks-EndOfScope-0.08, p5-Carp-Clan-6.00, p5-Class-C3-0.21, p5-Class-MOP-0.86, p5-Class-Singleton-1.4, p5-Data-OptList-0.104, p5-Date-Manip-5.54, p5-DateTime-0.49, p5-DateTime-Format-DateManip-0.04, p5-DateTime-Locale-0.42, p5-DateTime-TimeZone-0.90, p5-Devel-GlobalDestruction-0.02, p5-Digest-HMAC-1.01, p5-Digest-SHA1-2.12, p5-Email-Valid-0.181, p5-IO-Socket-INET6-2.56, p5-List-MoreUtils-0.22, p5-MRO-Compat-0.11, p5-Mail-Tools-2.04, p5-Math-BigInt-1.89, p5-Moose-0.81, p5-Moose-Policy-0.03, p5-MooseX-Types-0.12, p5-Net-DNS-0.65, p5-Net-Domain-TLD-1.68, p5-Net-IP-1.25, p5-Params-Coerce-0.14, p5-Params-Util-1.00, p5-Params-Validate-0.91, p5-Parse-RecDescent-1.96.0_2, p5-Scalar-List-Utils-1.21,1, p5-Scope-Guard-0.03, p5-Socket6-0.23, p5-Sub-Exporter-0.982, p5-Sub-Identify-0.04, p5-Sub-Install-0.925, p5-Sub-Name-0.04, p5-Sub-Uplevel-0.2002, p5-Task-Weaken-1.03, p5-Test-Exception-0.27, p5-Test-Simple-0.90, p5-Text-CSV_XS-0.63, p5-TimeDate-1.16,1, p5-URI-1.38, p5-Variable-Magic-0.35, p5-namespace-clean-0.11, p5-version-0.76, perl-5.8.9_3
Also listed in: Perl5

p5-Bio-Phylo-0.16
Phylogenetic analysis using perl
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, graphviz-2.22.2, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libltdl-1.5.26, libpthread-stubs-0.1, libxcb-1.3, mysql-client-5.0.83, p5-AcePerl-1.92, p5-Algorithm-Munkres-0.08, p5-Array-Compare-1.18, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Class-Data-Inheritable-0.08, p5-Clone-0.31, p5-Compress-Raw-Zlib-2.020, p5-Compress-Zlib-2.015, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.74, p5-Crypt-SSLeay-0.57, p5-DBD-mysql-4.012, p5-DBI-1.60.7, p5-Data-Stag-0.11, p5-Devel-StackTrace-1.21, p5-Digest-MD5-2.39, p5-Digest-SHA1-2.12, p5-Email-Date-Format-1.002, p5-Error-0.17015, p5-Exception-Class-1.29, p5-ExtUtils-CBuilder-0.24, p5-ExtUtils-ParseXS-2.19_1, p5-File-NFSLock-1.20, p5-File-Temp-0.22, p5-GD-2.43, p5-GD-SVG-0.33, p5-Graph-0.91,1, p5-GraphViz-2.04, p5-HTML-Parser-3.61, p5-HTML-Tagset-3.20, p5-HTML-Tree-3.23, p5-Heap-0.80, p5-IO-Compress-Base-2.015, p5-IO-Compress-Zlib-2.015, p5-IO-Socket-SSL-1.25, p5-IO-String-1.08, p5-IO-Tty-1.08, p5-IO-stringy-2.110, p5-IPC-Run-0.82, p5-IPC-ShareLite-0.17, p5-MIME-Base64-3.08, p5-MIME-Lite-3.02.4, p5-MIME-Tools-5.427_1,2, p5-MIME-Types-1.27, p5-Mail-Tools-2.04, p5-Math-Random-0.71, p5-Module-Build-0.33, p5-Net-SSLeay-1.35_1, p5-OLE-Storage_Lite-0.18, p5-Parse-RecDescent-1.96.0_2, p5-PostScript-0.06, p5-SOAP-Lite-0.710.08_1, p5-SVG-2.49, p5-SVG-Graph-0.02, p5-Scalar-List-Utils-1.21,1, p5-Set-Scalar-1.24, p5-Spreadsheet-ParseExcel-0.49,1, p5-Storable-2.20, p5-Test-Harness-3.17, p5-Text-Iconv-1.7, p5-Text-ParseWords-3.27, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-TimeDate-1.16,1, p5-URI-1.38, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.10, p5-XML-Parser-2.36, p5-XML-RegExp-0.03, p5-XML-SAX-0.96, p5-XML-SAX-Expat-0.40, p5-XML-SAX-Writer-0.52, p5-XML-Simple-2.18, p5-XML-Twig-3.32, p5-XML-Writer-0.606, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.12, p5-YAML-0.68, p5-bioperl-1.6.0, p5-libwww-5.828, p5-libxml-0.08, p5-version-0.76, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Perl5

p5-bioperl-1.6.0
A collection of Perl modules for bioinformatics
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: expat-2.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, graphviz-2.22.2, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libltdl-1.5.26, libpthread-stubs-0.1, libxcb-1.3, mysql-client-5.0.83, p5-AcePerl-1.92, p5-Algorithm-Munkres-0.08, p5-Array-Compare-1.18, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Clone-0.31, p5-Compress-Raw-Zlib-2.020, p5-Compress-Zlib-2.015, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.74, p5-Crypt-SSLeay-0.57, p5-DBD-mysql-4.012, p5-DBI-1.60.7, p5-Data-Stag-0.11, p5-Digest-MD5-2.39, p5-Digest-SHA1-2.12, p5-Email-Date-Format-1.002, p5-Error-0.17015, p5-ExtUtils-CBuilder-0.24, p5-ExtUtils-ParseXS-2.19_1, p5-File-NFSLock-1.20, p5-File-Temp-0.22, p5-GD-2.43, p5-GD-SVG-0.33, p5-Graph-0.91,1, p5-GraphViz-2.04, p5-HTML-Parser-3.61, p5-HTML-Tagset-3.20, p5-HTML-Tree-3.23, p5-Heap-0.80, p5-IO-Compress-Base-2.015, p5-IO-Compress-Zlib-2.015, p5-IO-Socket-SSL-1.25, p5-IO-String-1.08, p5-IO-Tty-1.08, p5-IO-stringy-2.110, p5-IPC-Run-0.82, p5-IPC-ShareLite-0.17, p5-MIME-Base64-3.08, p5-MIME-Lite-3.02.4, p5-MIME-Tools-5.427_1,2, p5-MIME-Types-1.27, p5-Mail-Tools-2.04, p5-Math-Random-0.71, p5-Module-Build-0.33, p5-Net-SSLeay-1.35_1, p5-OLE-Storage_Lite-0.18, p5-Parse-RecDescent-1.96.0_2, p5-PostScript-0.06, p5-SOAP-Lite-0.710.08_1, p5-SVG-2.49, p5-SVG-Graph-0.02, p5-Scalar-List-Utils-1.21,1, p5-Set-Scalar-1.24, p5-Spreadsheet-ParseExcel-0.49,1, p5-Storable-2.20, p5-Test-Harness-3.17, p5-Text-Iconv-1.7, p5-Text-ParseWords-3.27, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-TimeDate-1.16,1, p5-URI-1.38, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.10, p5-XML-Parser-2.36, p5-XML-RegExp-0.03, p5-XML-SAX-0.96, p5-XML-SAX-Expat-0.40, p5-XML-SAX-Writer-0.52, p5-XML-Simple-2.18, p5-XML-Twig-3.32, p5-XML-Writer-0.606, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.12, p5-YAML-0.68, p5-libwww-5.828, p5-libxml-0.08, p5-version-0.76, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Perl5

p5-bioperl-run-1.6.1
Wrapper modules for common bioinformatics tools
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: expat-2.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gd-2.0.35,1, gettext-0.17_1, graphviz-2.22.2, jpeg-6b_7, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libltdl-1.5.26, libpthread-stubs-0.1, libxcb-1.3, mysql-client-5.0.83, p5-AcePerl-1.92, p5-Algorithm-Diff-1.1902, p5-Algorithm-Munkres-0.08, p5-Array-Compare-1.18, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-2.04_1, p5-Cache-Cache-1.06, p5-Class-AutoClass-1.01, p5-Clone-0.31, p5-Compress-Raw-Zlib-2.020, p5-Compress-Zlib-2.015, p5-Convert-BinHex-1.119, p5-Convert-Binary-C-0.74, p5-Crypt-SSLeay-0.57, p5-DBD-mysql-4.012, p5-DBI-1.60.7, p5-Data-Stag-0.11, p5-Digest-MD5-2.39, p5-Digest-SHA1-2.12, p5-Email-Date-Format-1.002, p5-Error-0.17015, p5-ExtUtils-CBuilder-0.24, p5-ExtUtils-ParseXS-2.19_1, p5-File-NFSLock-1.20, p5-File-Temp-0.22, p5-GD-2.43, p5-GD-SVG-0.33, p5-Graph-0.91,1, p5-GraphViz-2.04, p5-HTML-Parser-3.61, p5-HTML-Tagset-3.20, p5-HTML-Tree-3.23, p5-Heap-0.80, p5-IO-Compress-Base-2.015, p5-IO-Compress-Zlib-2.015, p5-IO-Socket-SSL-1.25, p5-IO-String-1.08, p5-IO-Tty-1.08, p5-IO-stringy-2.110, p5-IPC-Run-0.82, p5-IPC-ShareLite-0.17, p5-MIME-Base64-3.08, p5-MIME-Lite-3.02.4, p5-MIME-Tools-5.427_1,2, p5-MIME-Types-1.27, p5-Mail-Tools-2.04, p5-Math-Random-0.71, p5-Module-Build-0.33, p5-Net-SSLeay-1.35_1, p5-OLE-Storage_Lite-0.18, p5-Parse-RecDescent-1.96.0_2, p5-PostScript-0.06, p5-SOAP-Lite-0.710.08_1, p5-SVG-2.49, p5-SVG-Graph-0.02, p5-Scalar-List-Utils-1.21,1, p5-Set-Scalar-1.24, p5-Spreadsheet-ParseExcel-0.49,1, p5-Storable-2.20, p5-Test-Harness-3.17, p5-Text-Iconv-1.7, p5-Text-ParseWords-3.27, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-TimeDate-1.16,1, p5-URI-1.38, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.14, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.10, p5-XML-Parser-2.36, p5-XML-RegExp-0.03, p5-XML-SAX-0.96, p5-XML-SAX-Expat-0.40, p5-XML-SAX-Writer-0.52, p5-XML-Simple-2.18, p5-XML-Twig-3.32, p5-XML-Writer-0.606, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.12, p5-YAML-0.68, p5-bioperl-1.6.0, p5-libwww-5.828, p5-libxml-0.08, p5-version-0.76, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Perl5

paml-4.2b
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Package | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

phd2fasta-0.990622.f
A converter from output files of Phred/Consed to FASTA files
Long description | Sources | Main Web Site
Maintained by: mzaki@biol.s.u-tokyo.ac.jp

phrap-0.990329
Phrap is a program for assembling shotgun DNA sequence data
Long description | Sources | Main Web Site
Maintained by: mzaki@biol.s.u-tokyo.ac.jp

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

phylip-3.68_1,1
A Phylogeny Inference Package
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-4.0.24, gettext-0.17_1, gmake-3.81_3, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXt-1.0.5_1, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, printproto-1.0.4, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

platon-2007.01.09_3
Tool for viewing molecular/crystallographic structures
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.3.4.20090621, kbproto-1.0.3, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libgmp-4.3.1, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, mpfr-2.4.1_1, pkg-config-0.23_1, python25-2.5.4_1, xcb-proto-1.5, xproto-7.0.15

povchem-1.0_3
Simple yet powerful tool to generate POV from a PDB file
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: jpeg-6b_7, kbproto-1.0.3, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, png-1.2.35, povray-3.6.1_4, python25-2.5.4_1, svgalib-1.4.3_5, tiff-3.8.2_3, xcb-proto-1.5, xproto-7.0.15
Also listed in: Graphics

primer3-1.1.3
Primer3 helps to choose primers for PCR reactions
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

protomol-2.0.3_3
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Package | Sources | Main Web Site
Maintained by: sangwoos@gmail.com
Requires: damageproto-1.1.0_2, dri2proto-2.0, expat-2.0.1, fixesproto-4.0, inputproto-1.5.0, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXi-1.2.1,1, libXmu-1.0.4,1, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libglut-7.4.4, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, png-1.2.35, python25-2.5.4_1, tiff-3.8.2_3, xcb-proto-1.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xproto-7.0.15

psi88-1.0_2
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.3.4.20090621, libgmp-4.3.1, libiconv-1.13, mpfr-2.4.1_1

py25-biopython-1.48
A collection of Python modules for bioinformatics
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: py25-mx-base-3.1.2, py25-numeric-24.2_3, py25-reportlab-1.21.2_1, python25-2.5.4_1
Also listed in: Python

pycogent-1.3.1
A toolkit for statistical analysis of biological sequences
Long description | Sources | Main Web Site
Maintained by: wenheping@gmail.com
Requires: blas-1.0_3, cython-0.11.2, gcc-4.3.4.20090621, gettext-0.17_1, lapack-3.2.1, libgmp-4.3.1, libiconv-1.13, mpfr-2.4.1_1, mysql-client-5.0.83, pkg-config-0.23_1, postgresql-client-8.2.13, py25-Jinja2-2.1.1, py25-MySQLdb-1.2.2, py25-docutils-0.5, py25-nose-0.10.4, py25-numpy-1.3.0,1, py25-psycopg2-2.0.11, py25-pygments-1.0, py25-pysqlite-2.3.5, py25-setuptools-0.6c9, py25-sphinx-0.6.2, py25-sqlalchemy-0.5.4.p2, python25-2.5.4_1, sqlite3-3.6.14.2
Also listed in: Python

pymol-1.0r2_3
Free and Open-Source molecular modeling system
Long description | Sources | Main Web Site
Maintained by: maho@FreeBSD.org
Requires: blt-2.4z_2, damageproto-1.1.0_2, dri2proto-2.0, expat-2.0.1, fixesproto-4.0, fontconfig-2.6.0,1, freetype2-2.3.9_1, gettext-0.17_1, gmake-3.81_3, inputproto-1.5.0, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXmu-1.0.4,1, libXrender-0.9.4_1, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libglut-7.4.4, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, pkg-config-0.23_1, png-1.2.35, py25-Pmw-1.3.2, py25-numeric-24.2_3, py25-tkinter-2.5.4_3, python25-2.5.4_1, renderproto-0.9.3, tcl-8.4.19_3,1, tcl-8.5.7_1, tcl-modules-8.5.7, tk-8.4.19_2,2, tk-8.5.7, xcb-proto-1.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xproto-7.0.15
Also listed in: Python

rasmol-2.7.2.1.1_3
Fast Molecular Visualization Program
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gccmakedep-1.0.2, imake-1.0.2_4,1, inputproto-1.5.0, kbproto-1.0.3, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXi-1.2.1,1, libpthread-stubs-0.1, libxcb-1.3, makedepend-1.0.1,1, perl-5.8.9_3, pkg-config-0.23_1, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xorg-cf-files-1.0.2_3, xproto-7.0.15

raster3d-2.7.d_1
A set of tools for generating raster images of proteins and molecules
Long description | Package | Sources | Main Web Site
Maintained by: shaun@FreeBSD.org
Requires: ImageMagick-6.5.3.10_1, cups-client-1.3.10_2, cups-image-1.3.10_2, expat-2.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gettext-0.17_1, ghostscript8-8.64_5, gio-fam-backend-2.20.4, glib-2.20.4, gnutls-2.6.5, gsfonts-8.11_5, jasper-1.900.1_7, jbigkit-1.6, jpeg-6b_7, kbproto-1.0.3, lcms-1.18a,1, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXt-1.0.5_1, libfpx-1.2.0.12_1, libgcrypt-1.4.4, libgpg-error-1.7, libiconv-1.13, liblqr-1-0.4.1, libltdl-1.5.26, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, pcre-7.9, perl-5.8.9_3, pkg-config-0.23_1, png-1.2.35, python25-2.5.4_1, tiff-3.8.2_3, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15
Also listed in: Graphics

recombine-1.41
A program to fit population models across sites
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

ruby18-bio-1.1.0
Integrated environment for Bioinformatics written in Ruby
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: ruby-1.8.7.160_3,1
Also listed in: Ruby

seaview-2006.02.13_3
Multiple DNA/protein sequence alignment editor
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: damageproto-1.1.0_2, dri2proto-2.0, expat-2.0.1, fixesproto-4.0, fltk-1.1.9, fontconfig-2.6.0,1, freetype2-2.3.9_1, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libX11-1.2.1_1,1, libXau-1.0.4, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXrender-0.9.4_1, libXxf86vm-1.0.2, libdrm-2.4.11, libpthread-stubs-0.1, libxcb-1.3, pdflib-7.0.3, pkg-config-0.23_1, png-1.2.35, python25-2.5.4_1, renderproto-0.9.3, xcb-proto-1.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xproto-7.0.15

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

sim4-2003.09.21
An algorithm for aligning expressed DNA with genomic sequences
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

ssaha-3.1c_1
Very fast matching and alignment of DNA sequences
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: gettext-0.17_1, gmake-3.81_3, libiconv-1.13

tRNAscan-SE-1.23_1
An improved tool for transfer RNA detection
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl-5.8.9_3

t_coffee-5.68
A multiple DNA or protein sequence alignment package
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: clustalw-2.0.6

tinker-4.2.20040908_3
A general purpose molecular modelling package
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.3.4.20090621, libgmp-4.3.1, libiconv-1.13, mpfr-2.4.1_1

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

treeviewx-0.5.1_3
A phylogenetic tree viewer
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: ORBit2-2.14.17, atk-1.26.0, bitstream-vera-1.10_4, cairo-1.8.8,1, compositeproto-0.4, damageproto-1.1.0_2, dbus-1.2.4.6, dbus-glib-0.80, dri2proto-2.0, encodings-1.0.2,1, expat-2.0.1, fixesproto-4.0, font-bh-ttf-1.0.0, font-misc-ethiopic-1.0.0, font-misc-meltho-1.0.0_1, font-util-1.0.1, fontconfig-2.6.0,1, freetype2-2.3.9_1, gamin-0.1.10_3, gconf2-2.26.2, gettext-0.17_1, gio-fam-backend-2.20.4, glib-2.20.4, gmake-3.81_3, gnome_subr-1.0, gnomehier-2.3_12, gstreamer-0.10.23, gstreamer-plugins-0.10.23,3, gtk-2.16.4, hicolor-icon-theme-0.10_2, inputproto-1.5.0, jasper-1.900.1_7, jpeg-6b_7, kbproto-1.0.3, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libIDL-0.8.13, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXcomposite-0.4.0,1, libXcursor-1.1.9_1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXrandr-1.3.0, libXrender-0.9.4_1, libXv-1.0.4,1, libXxf86vm-1.0.2, libdrm-2.4.11, libfontenc-1.0.4, libiconv-1.13, libmspack-0.0.20060920, liboil-0.3.16, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, mkfontdir-1.0.4, mkfontscale-1.0.6, pango-1.24.4, pcre-7.9, perl-5.8.9_3, pixman-0.15.4, pkg-config-0.23_1, png-1.2.35, policykit-0.9_4, popt-1.14, python25-2.5.4_1, randrproto-1.3.0, renderproto-0.9.3, shared-mime-info-0.60_1, tiff-3.8.2_3, videoproto-2.2.2, wxgtk2-2.8.10, wxgtk2-common-2.8.10, wxgtk2-contrib-2.8.10, wxgtk2-contrib-common-2.8.10, xcb-proto-1.5, xcb-util-0.3.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xineramaproto-1.1.2, xorg-fonts-truetype-7.4, xproto-7.0.15

wise-2.2.0
Intelligent algorithms for DNA searches
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

wu-blast-2.0_20060322
WU BLAST, a software package for sequence similarity searches
Long description | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar

xdrawchem-1.9.9_6
Chemical drawing program
Long description | Package | Sources | Main Web Site
Maintained by: hemi@puresimplicity.net
Requires: boost-python-1.37.0_1, cups-client-1.3.10_2, damageproto-1.1.0_2, dri2proto-2.0, expat-2.0.1, fixesproto-4.0, fontconfig-2.6.0,1, freetype2-2.3.9_1, gettext-0.17_1, gmake-3.81_3, gnutls-2.6.5, inputproto-1.5.0, jpeg-6b_7, kbproto-1.0.3, lcms-1.18a,1, libGL-7.4.4, libGLU-7.4.4, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXaw-1.0.5_1,1, libXdamage-1.1.1, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXfixes-4.0.3_1, libXft-2.1.13, libXi-1.2.1,1, libXinerama-1.0.3,1, libXmu-1.0.4,1, libXp-1.0.0,1, libXpm-3.5.7, libXrender-0.9.4_1, libXt-1.0.5_1, libXxf86vm-1.0.2, libdrm-2.4.11, libgcrypt-1.4.4, libgpg-error-1.7, libiconv-1.13, libmng-1.0.10, libpthread-stubs-0.1, libxcb-1.3, libxml2-2.7.3, nas-1.9.1_3, openbabel-2.2.1, pkg-config-0.23_1, png-1.2.35, printproto-1.0.4, python25-2.5.4_1, qt-3.3.8_9, renderproto-0.9.3, xcb-proto-1.5, xextproto-7.0.5, xf86vidmodeproto-2.2.2, xineramaproto-1.1.2, xproto-7.0.15

xmolwt-0.7_4
Calculate formula weight and percent of each element for a given formula
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-0.17_1, glib-1.2.10_12, gmake-3.81_3, gtk-1.2.10_20, inputproto-1.5.0, kbproto-1.0.3, libICE-1.0.4_1,1, libSM-1.1.0_1,1, libX11-1.2.1_1,1, libXau-1.0.4, libXdmcp-1.0.2_1, libXext-1.0.5,1, libXi-1.2.1,1, libiconv-1.13, libpthread-stubs-0.1, libxcb-1.3, perl-5.8.9_3, pkg-config-0.23_1, python25-2.5.4_1, xcb-proto-1.5, xextproto-7.0.5, xproto-7.0.15

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