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FreeBSD Ports: Biology

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Software related to biology.

InsightToolkit-2.8.1
Insight Toolkit
Long description | Sources | Main Web Site
Maintained by: bacon@smithers.neuro.mcw.edu
Requires: cmake-2.4.4, ldconfig_compat-1.0_8, rc_subr-1.31_1
Also listed in: Science

LBreeder-1.0_7
Allows you to display and breed L-system forms
Long description | Package | Sources | Main Web Site
Maintained by: dyeske@yahoo.com
Requires: XFree86-fontEncodings-4.5.0_1, XFree86-fontScalable-4.5.0_1, XFree86-libraries-4.5.0, atk-1.12.4, bitstream-vera-1.10_2, cairo-1.2.6_1, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, glib-2.12.9, gmake-3.81_1, gtk-2.10.9, hicolor-icon-theme-0.9_2, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libglut-6.4.2, libiconv-1.9.2_2, libxml2-2.6.27, pango-1.14.10, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, shared-mime-info-0.19, tiff-3.8.2_1, wxgtk2-2.4.2_14

adun-0.6
Molecular Simulator for GNUstep
Long description | Package | Sources | Main Web Site
Maintained by: gurkan@linuks.mine.nu
Requires: XFree86-libraries-4.5.0, aspell-0.60.5, cups-base-1.2.7_2, expat-2.0.0_1, ffcall-1.10_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gcc-4.1.2_20070129, gettext-0.14.5_2, gmake-3.81_1, gnustep-back-0.11.0, gnustep-base-1.13.1, gnustep-gui-0.11.0, gnustep-make-1.13.0_4, gnutls-1.6.1, gsl-1.8, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libaudiofile-0.2.6, libgcrypt-1.2.3_1, libgmp-4.2.1_1, libgpg-error-1.4, libiconv-1.9.2_2, libungif-4.1.4_2, libxml2-2.6.27, libxslt-1.1.20, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, tiff-3.8.2_1
Also listed in: Gnustep

afni-2006.06.30.1332
Advanced Functional Neuro Imaging
Long description | Package | Sources | Main Web Site
Maintained by: bacon@smithers.neuro.mcw.edu
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, gmake-3.81_1, imake-4.5.0, jbigkit-1.6, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mpeg_encode-1.5b, netpbm-10.26.38, open-motif-2.2.3_2, p5-File-Temp-0.18, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, tiff-3.8.2_1, whirlgif-3.04
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: expat-2.0.0_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

artemis-7_1
A DNA sequence viewer and annotation tool
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: desktop-file-utils-0.12, expat-2.0.0_1, gettext-0.14.5_2, glib-2.12.9, javavmwrapper-2.3, jdk-1.5.0p4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, nspr-4.6.4, pkg-config-0.21, popt-1.7_2, rc_subr-1.31_1
Also listed in: Java

avida-2.4.3
Avida is an auto-adaptive genetic system designed for ALife research
Long description | Package | Sources | Main Web Site
Maintained by: sf@slappy.org
Requires: cmake-2.4.4

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_9

biococoa-1.6.0
Bioinformatics framework
Long description | Package | Sources | Main Web Site
Maintained by: dinoex@FreeBSD.org
Requires: XFree86-libraries-4.5.0, aspell-0.60.5, cups-base-1.2.7_2, expat-2.0.0_1, ffcall-1.10_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gcc-4.1.2_20070129, gettext-0.14.5_2, gmake-3.81_1, gnustep-back-0.11.0, gnustep-base-1.13.1, gnustep-gui-0.11.0, gnustep-make-1.13.0_4, gnutls-1.6.1, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libaudiofile-0.2.6, libgcrypt-1.2.3_1, libgmp-4.2.1_1, libgpg-error-1.4, libiconv-1.9.2_2, libungif-4.1.4_2, libxml2-2.6.27, libxslt-1.1.20, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, tiff-3.8.2_1
Also listed in: Gnustep

biojava-1.5.b,1
Open-source java tools for processing biological data
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: apache-ant-1.6.5_2, desktop-file-utils-0.12, expat-2.0.0_1, gettext-0.14.5_2, glib-2.12.9, hsqldb-1.8.0.7, jakarta-commons-cli-1.0,1, jakarta-commons-collections-3.2, jakarta-commons-dbcp-1.2.1, jakarta-commons-pool-1.3, jakarta-regexp-1.4, javavmwrapper-2.3, jdk-1.5.0p4, junit-3.8.2, ldconfig_compat-1.0_8, libiconv-1.9.2_2, nspr-4.6.4, pkg-config-0.21, popt-1.7_2, rc_subr-1.31_1, xerces-j-2.8.0
Also listed in: Java

blat-33
A fast tool for local sequence similarity searches
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: expat-2.0.0_1, gcc-3.4.6,1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

boinc-simap-5.10.5.09
Similarity Matrix of Proteins project for BOINC
Long description | Package | Sources | Main Web Site
Maintained by: pav@FreeBSD.org
Requires: XFree86-fontEncodings-4.5.0_1, XFree86-fontScalable-4.5.0_1, XFree86-libraries-4.5.0, atk-1.12.4, bitstream-vera-1.10_2, boinc-client-5.4.9_1, cairo-1.2.6_1, curl-7.16.0_1, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, glib-2.12.9, gnomehier-2.2, gstreamer-plugins80-0.8.12_2,1, gstreamer80-0.8.12_2, gtk-2.10.9, hicolor-icon-theme-0.9_2, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libglut-6.4.2, libgnugetopt-1.2_1, libiconv-1.9.2_2, libmspack-0.0.20040308_3, libxml2-2.6.27, pango-1.14.10, pkg-config-0.21, png-1.2.14, popt-1.7_2, rc_subr-1.31_1, shared-mime-info-0.19, tiff-3.8.2_1, wxgtk2-2.6.3_2, wxgtk2-common-2.6.3_2

chemeq-1.50
Outputs LaTeX code for chemical reaction
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bison-1.75_2,1, expat-2.0.0_1, gettext-0.14.5_2, ldconfig_compat-1.0_8, libiconv-1.9.2_2, m4-1.4.8_1, rc_subr-1.31_1
Also listed in: Textproc

clustalw-1.83
CLUSTAL W Multiple Sequence Alignment Program
Long description | Package | Sources | Main Web Site
Maintained by: dbader@eece.unm.edu

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

cycle-0.3.1_1
A calendar program for women
Long description | Package | Sources | Main Web Site
Maintained by: danfe@FreeBSD.org
Requires: XFree86-fontEncodings-4.5.0_1, XFree86-fontScalable-4.5.0_1, XFree86-libraries-4.5.0, atk-1.12.4, bitstream-vera-1.10_2, cairo-1.2.6_1, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, glib-2.12.9, gnomehier-2.2, gstreamer-plugins80-0.8.12_2,1, gstreamer80-0.8.12_2, gtk-2.10.9, hicolor-icon-theme-0.9_2, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libglut-6.4.2, libgnugetopt-1.2_1, libiconv-1.9.2_2, libmspack-0.0.20040308_3, libxml2-2.6.27, pango-1.14.10, pkg-config-0.21, png-1.2.14, popt-1.7_2, py24-imaging-1.1.5_2, py24-numeric-24.2, py24-opengl-2.0.1.07_3, py24-tkinter-2.4.3_1, py24-wxPython-2.6.3.3, py24-wxPython-common-2.6.3.3, python24-2.4.3_3, rc_subr-1.31_1, shared-mime-info-0.19, tcl-8.4.14,1, tiff-3.8.2_1, tk-8.4.14,2, wxgtk2-2.6.3_2, wxgtk2-common-2.6.3_2, wxgtk2-contrib-2.6.3_1, wxgtk2-contrib-common-2.6.3_1
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
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 | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: linux_base-fc-4_9

embassy-3.0.0
A collection of contributed EMBOSS applications
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: XFree86-libraries-4.5.0, emboss-3.0.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gd-2.0.33_4,1, gettext-0.14.5_2, gmake-3.81_1, imake-4.5.0, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, open-motif-2.2.3_2, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1

emboss-3.0.0
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: XFree86-libraries-4.5.0, clustalw-1.83, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gd-2.0.33_4,1, gettext-0.14.5_2, gmake-3.81_1, imake-4.5.0, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, libtool-1.5.22_3, open-motif-2.2.3_2, pkg-config-0.21, png-1.2.14, primer3-1.0.1, rc_subr-1.31_1

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

fasta3-34.t26.b3
A collection of programs for searching DNA and protein databases
Long description | Package | 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: expat-2.0.0_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

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_9

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

garlic-1.5
Molecular viewer, editor and visualization program
Long description | Package | Sources | Main Web Site
Maintained by: maho@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, pkg-config-0.21, rc_subr-1.31_1

genpak-0.26_3
A set of small utilities to manipulate DNA sequences
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, gettext-0.14.5_2, gmake-3.81_1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1

gff2ps-0.98d_1
Converts gff-formated genomic data-sets to PostScript
Long description | Package | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au
Requires: bash-3.1.17, expat-2.0.0_1, gawk-3.1.1_1, gettext-0.14.5_2, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

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: expat-2.0.0_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

gperiodic-2.0.8_3
Displays a periodic table of the elements
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-fontEncodings-4.5.0_1, XFree86-fontScalable-4.5.0_1, XFree86-libraries-4.5.0, atk-1.12.4, bitstream-vera-1.10_2, cairo-1.2.6_1, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, glib-2.12.9, gnomehier-2.2, gtk-2.10.9, hicolor-icon-theme-0.9_2, intltool-0.35.4, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libiconv-1.9.2_2, libxml2-2.6.27, p5-XML-Parser-2.34_2, pango-1.14.10, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, shared-mime-info-0.19, tiff-3.8.2_1

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.0.0_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

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

jalview-2.07
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-1.6.5_2, desktop-file-utils-0.12, expat-2.0.0_1, gettext-0.14.5_2, glib-2.12.9, javavmwrapper-2.3, jdk-1.5.0p4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, nspr-4.6.4, pkg-config-0.21, popt-1.7_2, rc_subr-1.31_1
Also listed in: Java

kinemage-5.79
A molecular visualization program with special functions
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, imake-4.5.0, ldconfig_compat-1.0_8, open-motif-2.2.3_2, pkg-config-0.21, rc_subr-1.31_1

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

lamarc-2001.08.06_1
A package of programs for computing population parameters
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: fluctuate-1.40, migrate-2.1.3, recombine-1.41

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: ldconfig_compat-1.0_8, libtool-1.5.22_3, rc_subr-1.31_1

linux-foldingathome-5.02
Distributed client for Protein Folding
Long description | Package | Sources | Main Web Site
Maintained by: onatan@gmail.com
Requires: linux_base-fc-4_9

lsysexp-0.67_5
A GTK based program for viewing and creating L-system fractals
Long description | Package | Sources | Main Web Site
Maintained by: dyeske@yahoo.com
Requires: XFree86-fontEncodings-4.5.0_1, XFree86-fontScalable-4.5.0_1, XFree86-libraries-4.5.0, atk-1.12.4, bitstream-vera-1.10_2, cairo-1.2.6_1, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, glib-2.12.9, gtk-2.10.9, hicolor-icon-theme-0.9_2, intltool-0.35.4, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, libiconv-1.9.2_2, libxml2-2.6.27, p5-XML-Parser-2.34_2, pango-1.14.10, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, shared-mime-info-0.19, tiff-3.8.2_1

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: fasta3-34.t26.b3

migrate-2.1.3
A program to estimate population sizes and migration rates
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org

minc-1.4_1
Medical Imaging NetCDF
Long description | Package | Sources | Main Web Site
Maintained by: bacon@smithers.neuro.mcw.edu
Requires: gcc-3.2.3_3, ldconfig_compat-1.0_8, libtool-1.5.22_3, netcdf-3.6.1, rc_subr-1.31_1
Also listed in: Science

minc-2.0.09
Medical Imaging NetCDF
Long description | Package | Sources | Main Web Site
Maintained by: bacon@smithers.neuro.mcw.edu
Requires: gcc-3.2.3_3, hdf5-1.6.5, ldconfig_compat-1.0_8, netcdf-3.6.1, rc_subr-1.31_1
Also listed in: Science

molden-4.4_3
Display molecular orbitals and electron densities in 2D and 3D
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gcc-4.2.0_20070124, ldconfig_compat-1.0_8, libglut-6.4.2, libgmp-4.2.1_1, libiconv-1.9.2_2, mpfr-2.2.1, pkg-config-0.21, rc_subr-1.31_1

mopac-7.1.10,1
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.0.0_1, f2c-20060810_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

nab-5.1.2
A language for macromolecules
Long description | Package | Sources | Main Web Site
Maintained by: mldodson@houston.rr.com
Requires: ucpp-1.3

ncbi-toolkit-2006.05.07
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: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, imake-4.5.0, ldconfig_compat-1.0_8, open-motif-2.2.3_2, pkg-config-0.21, rc_subr-1.31_1

ortep3-1.0.3_3
The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.2.0_20070124, ldconfig_compat-1.0_8, libgmp-4.2.1_1, libiconv-1.9.2_2, mpfr-2.2.1, rc_subr-1.31_1

p5-AcePerl-1.91
Perl5 interface to the ACEDB genome database system
Long description | Package | Sources | Main Web Site
Maintained by: pgollucci@p6m7g8.com
Requires: p5-Cache-Cache-1.05, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-PathTools-3.24, p5-Scalar-List-Utils-1.19,1, p5-Storable-2.15, p5-XSLoader-0.07
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
Also listed in: Perl5

p5-Bio-Das-1.03
Client-side library for Distributed Genome Annotation System
Long description | Package | Sources | Main Web Site
Maintained by: razi@genet.sickkids.on.ca
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mysql-client-5.0.33, p5-AcePerl-1.91, p5-Cache-Cache-1.05, p5-Compress-Raw-Zlib-2.003, p5-Compress-Zlib-2.003, p5-Convert-BinHex-1.119, p5-Crypt-SSLeay-0.53, p5-DBD-mysql-4.0000, p5-DBI-1.37_1, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-File-Temp-0.18, p5-GD-2.35, p5-HTML-Parser-3.56, p5-HTML-Tagset-3.10, p5-HTML-Tree-3.23, p5-IO-Compress-Base-2.003, p5-IO-Compress-Zlib-2.003, p5-IO-Socket-SSL-1.02, p5-IO-String-1.08, p5-IO-stringy-2.110, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-MIME-Lite-3.01, p5-MIME-Tools-5.420,2, p5-Mail-Tools-1.74, p5-Net-1.19,1, p5-Net-SSLeay-1.30_1, p5-Parse-RecDescent-1.94, p5-PathTools-3.24, p5-Pod-Parser-1.35, p5-SOAP-Lite-0.69, p5-Scalar-List-Utils-1.19,1, p5-Storable-2.15, p5-Test-Harness-2.64, p5-Test-Simple-0.67, p5-Text-Balanced-2.0.0_1, p5-Text-Iconv-1.4, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-URI-1.35, p5-XML-DOM-1.44, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.09_1, p5-XML-Node-0.11, p5-XML-Parser-2.34_2, p5-XML-RegExp-0.03, p5-XML-SAX-0.14, p5-XML-SAX-Writer-0.50, p5-XML-Simple-2.16, p5-XML-Twig-3.29, p5-XML-Writer-0.602, p5-XML-XPath-1.13, p5-XSLoader-0.07, p5-bioperl-1.4, p5-libwww-5.805, p5-libxml-0.08, p5-version-0.69, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, readline-5.2

p5-Bio-Phylo-0.15
Phylogenetic analysis using perl
Long description | Package | Sources | Main Web Site
Maintained by: aaron@FreeBSD.org
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mysql-client-5.0.33, p5-AcePerl-1.91, p5-Archive-Tar-1.30, p5-Cache-Cache-1.05, p5-Class-Data-Inheritable-0.06, p5-Compress-Raw-Zlib-2.003, p5-Compress-Zlib-2.003, p5-Convert-BinHex-1.119, p5-Crypt-SSLeay-0.53, p5-DBD-mysql-4.0000, p5-DBI-1.37_1, p5-Devel-StackTrace-1.13, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-Exception-Class-1.23_1, p5-ExtUtils-CBuilder-0.18, p5-ExtUtils-ParseXS-2.17, p5-File-Temp-0.18, p5-Filter-1.32, p5-GD-2.35, p5-HTML-Parser-3.56, p5-HTML-Tagset-3.10, p5-HTML-Tree-3.23, p5-IO-Compress-Base-2.003, p5-IO-Compress-Zlib-2.003, p5-IO-Socket-SSL-1.02, p5-IO-String-1.08, p5-IO-Zlib-1.04_1, p5-IO-stringy-2.110, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-MIME-Lite-3.01, p5-MIME-Tools-5.420,2, p5-Mail-Tools-1.74, p5-Math-Random-0.69, p5-Module-Build-0.28.06, p5-Net-1.19,1, p5-Net-SSLeay-1.30_1, p5-Parse-RecDescent-1.94, p5-PathTools-3.24, p5-Pod-Escapes-1.04, p5-Pod-Parser-1.35, p5-Pod-Simple-3.04, p5-SOAP-Lite-0.69, p5-SVG-2.33, p5-Scalar-List-Utils-1.19,1, p5-Spiffy-0.30, p5-Storable-2.15, p5-Term-ANSIColor-1.11, p5-Test-Base-0.53, p5-Test-Harness-2.64, p5-Test-Simple-0.67, p5-Text-Balanced-2.0.0_1, p5-Text-Iconv-1.4, p5-Text-Shellwords-1.08, p5-Text-Tabs+Wrap-2006.1117, p5-Tie-IxHash-1.21, p5-URI-1.35, p5-XML-DOM-1.44, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.09_1, p5-XML-Node-0.11, p5-XML-Parser-2.34_2, p5-XML-RegExp-0.03, p5-XML-SAX-0.14, p5-XML-SAX-Writer-0.50, p5-XML-Simple-2.16, p5-XML-Twig-3.29, p5-XML-Writer-0.602, p5-XML-XPath-1.13, p5-XSLoader-0.07, p5-YAML-0.62, p5-bioperl-1.4, p5-libwww-5.805, p5-libxml-0.08, p5-podlators-2.0.5, p5-version-0.69, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, readline-5.2
Also listed in: Perl5

p5-bioperl-1.4
A collection of Perl modules for bioinformatics
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mysql-client-5.0.33, p5-AcePerl-1.91, p5-Cache-Cache-1.05, p5-Compress-Raw-Zlib-2.003, p5-Compress-Zlib-2.003, p5-Convert-BinHex-1.119, p5-Crypt-SSLeay-0.53, p5-DBD-mysql-4.0000, p5-DBI-1.37_1, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-File-Temp-0.18, p5-GD-2.35, p5-HTML-Parser-3.56, p5-HTML-Tagset-3.10, p5-HTML-Tree-3.23, p5-IO-Compress-Base-2.003, p5-IO-Compress-Zlib-2.003, p5-IO-Socket-SSL-1.02, p5-IO-String-1.08, p5-IO-stringy-2.110, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-MIME-Lite-3.01, p5-MIME-Tools-5.420,2, p5-Mail-Tools-1.74, p5-Net-1.19,1, p5-Net-SSLeay-1.30_1, p5-Parse-RecDescent-1.94, p5-PathTools-3.24, p5-Pod-Parser-1.35, p5-SOAP-Lite-0.69, p5-Scalar-List-Utils-1.19,1, p5-Storable-2.15, p5-Test-Harness-2.64, p5-Test-Simple-0.67, p5-Text-Balanced-2.0.0_1, p5-Text-Iconv-1.4, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-URI-1.35, p5-XML-DOM-1.44, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.09_1, p5-XML-Node-0.11, p5-XML-Parser-2.34_2, p5-XML-RegExp-0.03, p5-XML-SAX-0.14, p5-XML-SAX-Writer-0.50, p5-XML-Simple-2.16, p5-XML-Twig-3.29, p5-XML-Writer-0.602, p5-XML-XPath-1.13, p5-XSLoader-0.07, p5-libwww-5.805, p5-libxml-0.08, p5-version-0.69, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, readline-5.2
Also listed in: Perl5

p5-bioperl-1.5.1
A collection of Perl modules for bioinformatics (developer release)
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mysql-client-5.0.33, p5-AcePerl-1.91, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-Cache-1.05, p5-Class-AutoClass-1.01, p5-Clone-0.22, p5-Compress-Raw-Zlib-2.003, p5-Compress-Zlib-2.003, p5-Convert-BinHex-1.119, p5-Crypt-SSLeay-0.53, p5-DBD-mysql-4.0000, p5-DBI-1.37_1, p5-Data-Stag-0.10, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-File-Temp-0.18, p5-GD-2.35, p5-GD-SVG-0.28, p5-Graph-0.81,1, p5-HTML-Parser-3.56, p5-HTML-Tagset-3.10, p5-HTML-Tree-3.23, p5-Heap-0.71, p5-IO-Compress-Base-2.003, p5-IO-Compress-Zlib-2.003, p5-IO-Socket-SSL-1.02, p5-IO-String-1.08, p5-IO-stringy-2.110, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-MIME-Lite-3.01, p5-MIME-Tools-5.420,2, p5-Mail-Tools-1.74, p5-Net-1.19,1, p5-Net-SSLeay-1.30_1, p5-PathTools-3.24, p5-SOAP-Lite-0.69, p5-SVG-2.33, p5-SVG-Graph-0.01, p5-Scalar-List-Utils-1.19,1, p5-Storable-2.15, p5-Text-Iconv-1.4, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-URI-1.35, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.13_1, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.09_1, p5-XML-Parser-2.34_2, p5-XML-RegExp-0.03, p5-XML-SAX-0.14, p5-XML-SAX-Writer-0.50, p5-XML-Simple-2.16, p5-XML-Twig-3.29, p5-XML-Writer-0.602, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.08, p5-XSLoader-0.07, p5-libwww-5.805, p5-libxml-0.08, perl-5.8.8, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, readline-5.2
Also listed in: Perl5

p5-bioperl-run-1.4
Wrapper modules for common bioinformatics tools
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mysql-client-5.0.33, p5-AcePerl-1.91, p5-Algorithm-Diff-1.1902, p5-Cache-Cache-1.05, p5-Compress-Raw-Zlib-2.003, p5-Compress-Zlib-2.003, p5-Convert-BinHex-1.119, p5-Crypt-SSLeay-0.53, p5-DBD-mysql-4.0000, p5-DBI-1.37_1, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-File-Temp-0.18, p5-GD-2.35, p5-HTML-Parser-3.56, p5-HTML-Tagset-3.10, p5-HTML-Tree-3.23, p5-IO-Compress-Base-2.003, p5-IO-Compress-Zlib-2.003, p5-IO-Socket-SSL-1.02, p5-IO-String-1.08, p5-IO-stringy-2.110, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-MIME-Lite-3.01, p5-MIME-Tools-5.420,2, p5-Mail-Tools-1.74, p5-Net-1.19,1, p5-Net-SSLeay-1.30_1, p5-Parse-RecDescent-1.94, p5-PathTools-3.24, p5-Pod-Parser-1.35, p5-SOAP-Lite-0.69, p5-Scalar-List-Utils-1.19,1, p5-Storable-2.15, p5-Test-Harness-2.64, p5-Test-Simple-0.67, p5-Text-Balanced-2.0.0_1, p5-Text-Iconv-1.4, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-URI-1.35, p5-XML-DOM-1.44, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.09_1, p5-XML-Node-0.11, p5-XML-Parser-2.34_2, p5-XML-RegExp-0.03, p5-XML-SAX-0.14, p5-XML-SAX-Writer-0.50, p5-XML-Simple-2.16, p5-XML-Twig-3.29, p5-XML-Writer-0.602, p5-XML-XPath-1.13, p5-XSLoader-0.07, p5-bioperl-1.4, p5-libwww-5.805, p5-libxml-0.08, p5-version-0.69, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, readline-5.2
Also listed in: Perl5

p5-bioperl-run-1.5.1
Wrapper modules for common bioinformatics tools (developer release)
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: expat-2.0.0_1, freetype2-2.2.1_1, gd-2.0.33_4,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, mysql-client-5.0.33, p5-AcePerl-1.91, p5-Algorithm-Diff-1.1902, p5-Bio-ASN1-EntrezGene-1.091, p5-Cache-Cache-1.05, p5-Class-AutoClass-1.01, p5-Clone-0.22, p5-Compress-Raw-Zlib-2.003, p5-Compress-Zlib-2.003, p5-Convert-BinHex-1.119, p5-Crypt-SSLeay-0.53, p5-DBD-mysql-4.0000, p5-DBI-1.37_1, p5-Data-Stag-0.10, p5-Digest-1.15, p5-Digest-MD5-2.36, p5-Digest-SHA1-2.11, p5-Error-0.17.008, p5-File-Temp-0.18, p5-GD-2.35, p5-GD-SVG-0.28, p5-Graph-0.81,1, p5-HTML-Parser-3.56, p5-HTML-Tagset-3.10, p5-HTML-Tree-3.23, p5-Heap-0.71, p5-IO-Compress-Base-2.003, p5-IO-Compress-Zlib-2.003, p5-IO-Socket-SSL-1.02, p5-IO-String-1.08, p5-IO-stringy-2.110, p5-IPC-ShareLite-0.09, p5-MIME-Base64-3.07, p5-MIME-Lite-3.01, p5-MIME-Tools-5.420,2, p5-Mail-Tools-1.74, p5-Net-1.19,1, p5-Net-SSLeay-1.30_1, p5-PathTools-3.24, p5-SOAP-Lite-0.69, p5-SVG-2.33, p5-SVG-Graph-0.01, p5-Scalar-List-Utils-1.19,1, p5-Storable-2.15, p5-Text-Iconv-1.4, p5-Text-Shellwords-1.08, p5-Tie-IxHash-1.21, p5-URI-1.35, p5-XML-DOM-1.44, p5-XML-DOM-XPath-0.13_1, p5-XML-Filter-BufferText-1.01, p5-XML-Handler-YAWriter-0.23, p5-XML-NamespaceSupport-1.09_1, p5-XML-Parser-2.34_2, p5-XML-RegExp-0.03, p5-XML-SAX-0.14, p5-XML-SAX-Writer-0.50, p5-XML-Simple-2.16, p5-XML-Twig-3.29, p5-XML-Writer-0.602, p5-XML-XPath-1.13, p5-XML-XPathEngine-0.08, p5-XSLoader-0.07, p5-bioperl-1.5.1, p5-libwww-5.805, p5-libxml-0.08, perl-5.8.8, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, readline-5.2
Also listed in: Perl5

paml-3.15
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Package | Sources | Main Web Site
Maintained by: dbader@eece.unm.edu
Requires: expat-2.0.0_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libiconv-1.9.2_2, rc_subr-1.31_1

phylip-3.66,1
A Phylogeny Inference Package
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, ldconfig_compat-1.0_8, pkg-config-0.21, rc_subr-1.31_1

platon-2007.01.09
Tool for viewing molecular/crystallographic structures
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gcc-4.2.0_20070124, ldconfig_compat-1.0_8, libgmp-4.2.1_1, libiconv-1.9.2_2, mpfr-2.2.1, pkg-config-0.21, rc_subr-1.31_1

povchem-1.0_2
Simple yet powerful tool to generate POV from a PDB file
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, jpeg-6b_4, ldconfig_compat-1.0_8, pkg-config-0.21, png-1.2.14, povray-3.6.1, rc_subr-1.31_1, svgalib-1.4.3_5, tiff-3.8.2_1
Also listed in: Graphics

primer3-1.0.1
Primer3 helps to choose primers for PCR reactions
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar

protomol-2.0.3
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Package | Sources | Main Web Site
Maintained by: sangwoos@gmail.com
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gcc-3.4.6,1, jpeg-6b_4, ldconfig_compat-1.0_8, libiconv-1.9.2_2, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, tiff-3.8.2_1

psi88-1.0_1
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.2.0_20070124, ldconfig_compat-1.0_8, libgmp-4.2.1_1, libiconv-1.9.2_2, mpfr-2.2.1, rc_subr-1.31_1

py24-biopython-1.42
A collection of Python modules for bioinformatics
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: py24-mx-base-2.0.6, py24-numeric-24.2, py24-reportlab-1.21.1, python24-2.4.3_3
Also listed in: Python

pymol-0.99rc1
Free and Open-Source molecular modeling system
Long description | Sources | Main Web Site
Maintained by: maho@FreeBSD.org
Requires: XFree86-libraries-4.5.0, blt-2.4z, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, gmake-3.81_1, ldconfig_compat-1.0_8, libglut-6.4.2, libiconv-1.9.2_2, pkg-config-0.21, png-1.2.14, py24-numeric-24.2, py24-pmw-1.2_1, py24-tkinter-2.4.3_1, python24-2.4.3_3, rc_subr-1.31_1, tcl-8.4.14,1, tk-8.4.14,2
Also listed in: Python

rasmol-2.7.2.1.1
Fast Molecular Visualization Program
Long description | Package | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, imake-4.5.0, ldconfig_compat-1.0_8, pkg-config-0.21, rc_subr-1.31_1

raster3d-2.7.d
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-6.3.2.0, XFree86-libraries-4.5.0, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, ghostscript-gnu-7.07_15, gsfonts-8.11_2, jasper-1.701.0_1, jbigkit-1.6, jpeg-6b_4, lcms-1.16_1,1, ldconfig_compat-1.0_8, libfpx-1.2.0.12, libiconv-1.9.2_2, libltdl-1.5.22_1, libxml2-2.6.27, mpeg2codec-1.2_1, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1, tiff-3.8.2_1
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-1.0.0
Integrated environment for Bioinformatics written in Ruby
Long description | Package | Sources | Main Web Site
Maintained by: mauricio@arareko.net
Requires: ldconfig_compat-1.0_8, rc_subr-1.31_1, ruby-1.8.5.12,1
Also listed in: Ruby

seaview-2006.02.13_1
Multiple DNA/protein sequence alignment editor
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: XFree86-libraries-4.5.0, expat-2.0.0_1, fltk-1.1.7_2, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, jpeg-6b_4, ldconfig_compat-1.0_8, libXft-2.1.7_1, pdflib-7.0.0p3, pkg-config-0.21, png-1.2.14, rc_subr-1.31_1

seqio-1.2.2
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

tRNAscan-SE-1.21
An improved tool for transfer RNA detection
Long description | Package | Sources | Main Web Site
Maintained by: chuynh@biolateral.com.au

t_coffee-3.27
A multiple DNA or protein sequence alignment package
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: clustalw-1.83

tinker-4.2.20040908_1
A general purpose molecular modelling package
Long description | Sources | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gcc-4.2.0_20070124, imake-4.5.0, ldconfig_compat-1.0_8, libgmp-4.2.1_1, libiconv-1.9.2_2, mpfr-2.2.1, rc_subr-1.31_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_1
A phylogenetic tree viewer
Long description | Package | Sources | Main Web Site
Maintained by: fernan@iib.unsam.edu.ar
Requires: ORBit2-2.14.5, XFree86-fontEncodings-4.5.0_1, XFree86-fontScalable-4.5.0_1, XFree86-libraries-4.5.0, atk-1.12.4, bitstream-vera-1.10_2, cairo-1.2.6_1, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gconf2-2.16.0, gettext-0.14.5_2, glib-2.12.9, gmake-3.81_1, gnomehier-2.2, gstreamer-0.10.11, gstreamer-plugins-0.10.11,2, gtk-2.10.9, hicolor-icon-theme-0.9_2, jpeg-6b_4, ldconfig_compat-1.0_8, libIDL-0.8.7, libXft-2.1.7_1, libgnugetopt-1.2_1, libiconv-1.9.2_2, libmspack-0.0.20040308_3, liboil-0.3.10_1, libxml2-2.6.27, linc-1.0.3_6, pango-1.14.10, pkg-config-0.21, png-1.2.14, popt-1.7_2, rc_subr-1.31_1, shared-mime-info-0.19, tiff-3.8.2_1, wxgtk2-2.8.0, wxgtk2-common-2.8.0, wxgtk2-contrib-2.8.0, wxgtk2-contrib-common-2.8.0

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_1
Chemical drawing program
Long description | Package | Sources | Main Web Site
Maintained by: hemi@puresimplicity.net
Requires: XFree86-libraries-4.5.0, cups-base-1.2.7_2, expat-2.0.0_1, fontconfig-2.3.2_6,1, freetype2-2.2.1_1, gettext-0.14.5_2, gmake-3.81_1, gnutls-1.6.1, jpeg-6b_4, lcms-1.16_1,1, ldconfig_compat-1.0_8, libXft-2.1.7_1, libgcrypt-1.2.3_1, libgpg-error-1.4, libiconv-1.9.2_2, libmng-1.0.9, libxml2-2.6.27, nas-1.8, openbabel-2.0.2, pkg-config-0.21, png-1.2.14, qt-3.3.6_3,