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Category listing - biology
Click to add this to your default watch list[s] Software related to biology.- Number of ports in this category: 91

Ports marked with a * actually reside within another category but have biology listed as a secondary category.


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InsightToolkit 2.8.1_2* search for ports that depend on this port
Insight Toolkit

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 07 Sep 2006 03:14:06
Also Listed In: science
License: not specified in port
afni 2012.04.17.2129_11* search for ports that depend on this port
Advanced Functional Neuro Imaging
Maintained by: jwbacon@tds.net search for ports maintained by this maintainer
Port Added: 25 Jan 2006 17:37:44
Also Listed In: science graphics
License: GPLv2
ariadne 1.3 search for ports that depend on this port
Programs to compare protein sequences and profiles

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Jun 2004 14:31:00
License: not specified in port
artemis 9_1 search for ports that depend on this port
DNA sequence viewer and annotation tool

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Dec 2001 11:39:40
Also Listed In: java
License: not specified in port
avida 2.12.4 search for ports that depend on this port
Auto-adaptive genetic system designed for ALife research

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 20 Apr 2002 15:17:56
License: GPLv3
babel 1.6_4 search for ports that depend on this port
Converts among various molecular file formats

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
Also Listed In: converters
License: not specified in port
biococoa 2.2.2_1 search for ports that depend on this port
Bioinformatics framework
Maintained by: theraven@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Dec 2006 09:21:22
Also Listed In: gnustep
License: LGPL21
biojava 1.7,1 search for ports that depend on this port
Open-source Java tools for processing biological data
Maintained by: wenheping@gmail.com search for ports maintained by this maintainer
Port Added: 10 Oct 2000 08:14:04
Also Listed In: java
License: not specified in port
blat 35 search for ports that depend on this port
Fast tool for local sequence similarity searches

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:29:12
License: not specified in port
boinc-simap 5.10.5.09_7 search for ports that depend on this port
Deprecated DEPRECATED: Project shutting down, see http://boincsimap.org/boincsimap/forum_thread.php?id=88
Expiration Date EXPIRATION DATE: 2015-01-01
Similarity Matrix of Proteins project for BOINC

There is no maintainer for this port.
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Port Added: 19 Jun 2006 20:34:29
License: not specified in port
chemeq 1.50_2 search for ports that depend on this port
Outputs LaTeX code for chemical reaction

There is no maintainer for this port.
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Port Added: 10 Jul 2000 00:14:19
Also Listed In: textproc
License: not specified in port
clustalw 2.1_1 search for ports that depend on this port
Restricted RESTRICTED: No commercial use.
Multiple alignment program for DNA or proteins

There is no maintainer for this port.
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Port Added: 10 Jul 2000 00:17:41
License: not specified in port
consed 27.0 search for ports that depend on this port
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request access permission via e-mail to get the tarball. Free for academic use.
Graphical tool for editing Phrap assemblies
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 24 May 2008 07:01:28
License: not specified in port
crux 1.2.0_5 search for ports that depend on this port
Software toolkit for phylogenetic inference

There is no maintainer for this port.
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Port Added: 08 Jun 2009 23:51:06
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE
cycle 0.3.1_9* search for ports that depend on this port
Calendar program for women

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Jun 2005 14:05:46
Also Listed In: deskutils python
License: GPLv2
emboss 6.6.0 search for ports that depend on this port
Collection of open source tools for genetic sequence analysis
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 31 Jul 2000 16:13:54
License: GPLv2
fasta 21.1.1 search for ports that depend on this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product
Collection of programs for searching DNA and protein databases

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 11 Feb 2001 13:24:20
License: not specified in port
fasta3 36.3.6d_1 search for ports that depend on this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product
Collection of programs for searching DNA and protein databases

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 11 Feb 2001 13:29:00
License: Fasta
fastdnaml 1.2.2_2 search for ports that depend on this port
Faster DNAML, makes phylogenetic trees using maximum likelihood

There is no maintainer for this port.
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Port Added: 12 Oct 2000 09:31:14
License: GPLv2
fluctuate 1.40 search for ports that depend on this port
Program to fit population models

There is no maintainer for this port.
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Port Added: 06 Aug 2001 11:45:39
License: not specified in port
garlic 1.6_1 search for ports that depend on this port
Molecular viewer, editor, and visualization program
Maintained by: maho@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Jul 2003 06:41:18
License: not specified in port
gff2ps 0.98d_2 search for ports that depend on this port
Converts gff-formated genomic data-sets to PostScript

There is no maintainer for this port.
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Port Added: 19 Dec 2001 07:03:28
License: GPLv2
gmap 2006.04.21_1 search for ports that depend on this port
Genomic Mapping and Alignment Program for mRNA and EST Sequences
Maintained by: rpz@cse.wustl.edu search for ports maintained by this maintainer
Port Added: 29 Sep 2006 04:09:50
License: not specified in port
gperiodic 2.0.10_7 search for ports that depend on this port
Displays a periodic table of the elements

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: not specified in port
grappa 2.0 search for ports that depend on this port
Genome Rearrangements Analysis and Phylogeny Software

There is no maintainer for this port.
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Port Added: 04 Jul 2001 05:39:40
License: not specified in port
hmmer 3.0 search for ports that depend on this port
Profile hidden Markov models for biological sequence analysis

There is no maintainer for this port.
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Port Added: unknown
License: not specified in port
iolib 1.13.7 search for ports that depend on this port
General purpose trace file (and Experiment File) reading interface
Maintained by: danilo@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Aug 2009 23:34:46
License: BSD3CLAUSE
jalview 2.07_2 search for ports that depend on this port
Viewer and editor for multiple sequence alignments

There is no maintainer for this port.
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Port Added: 13 Feb 2006 09:43:01
Also Listed In: java
License: not specified in port
lagan 2.0 search for ports that depend on this port
Efficient tools for large-scale multiple alignments of genomic DNA

There is no maintainer for this port.
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Port Added: 16 Mar 2006 22:31:50
License: GPLv2
lamarc 2.1.8,1 search for ports that depend on this port
Package of programs for computing population parameters

There is no maintainer for this port.
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Port Added: 07 Aug 2001 05:17:58
License: APACHE20
libsbml 5.10.2 search for ports that depend on this port
API Library for Working with SBML File

There is no maintainer for this port.
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Port Added: 28 May 2009 23:36:42
Also Listed In: devel
License: LGPL21
linux-foldingathome 5.04 search for ports that depend on this port
Distributed client for Protein Folding
Maintained by: onatan@gmail.com search for ports maintained by this maintainer
Port Added: 28 Aug 2006 22:34:01
License: not specified in port
mafft 7.149 search for ports that depend on this port
Multiple alignment program for amino acid or nucleotide sequences
Maintained by: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:41:45
License: BSD2CLAUSE
mapm3 3.0 search for ports that depend on this port
Constructs linkage maps of markers segregating in experimental crosses
Maintained by: tphilipp@potion-studios.com search for ports maintained by this maintainer
Port Added: 06 Apr 2008 04:49:23
License: not specified in port
migrate 3.5.1 search for ports that depend on this port
Program to estimate population sizes and migration rates
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 Aug 2001 10:07:46
License: not specified in port
minc2 2.2.00,1* search for ports that depend on this port
Medical Imaging NetCDF

There is no maintainer for this port.
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Port Added: 30 Apr 2006 12:09:06
Also Listed In: science
License: BSD
molden 5.0.7_2,1 search for ports that depend on this port
Restricted RESTRICTED: free for academic, non profit usage; do not re-distribute source and executable.
Display molecular orbitals and electron densities in 2D and 3D

There is no maintainer for this port.
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Port Added: unknown
License: not specified in port
mopac 7.1.11_4,1 search for ports that depend on this port
Semi-empirical (MNDO, etc.) molecular orbital calculation

There is no maintainer for this port.
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Port Added: unknown
License: not specified in port
mrbayes 3.1.2_1 search for ports that depend on this port
Bayesian inference of phylogeny
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 15 Dec 2007 15:13:49
License: not specified in port
mummer 3.23_1 search for ports that depend on this port
Modular system for rapid whole genome alignment

There is no maintainer for this port.
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Port Added: 14 Dec 2007 20:56:11
License: not specified in port
muscle 3.8.31 search for ports that depend on this port
MUltiple Sequence Comparison by Log-Expectation
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 14 May 2008 13:52:50
License: not specified in port
ncbi-toolkit 2012.06.20 search for ports that depend on this port
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support

There is no maintainer for this port.
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Port Added: 29 Oct 2000 10:56:24
License: not specified in port
njplot 2.1_3 search for ports that depend on this port
Phylogenetic tree drawing program capable of interactive manipulation
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 14 May 2008 14:07:25
License: not specified in port
ortep3 1.0.3_9 search for ports that depend on this port
Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure

There is no maintainer for this port.
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Port Added: unknown
License: not specified in port
p5-AcePerl 1.92_2 search for ports that depend on this port
Perl5 interface to the ACEDB genome database system

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Port Added: 28 Jul 2000 10:16:10
Also Listed In: databases perl5
License: not specified in port
p5-Bio-ASN1-EntrezGene 1.091 search for ports that depend on this port
Regular expression-based Perl Parser for NCBI Entrez Gene
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 15 Oct 2005 20:11:03
Also Listed In: perl5
License: not specified in port
p5-Bio-Das 1.17_2 search for ports that depend on this port
Client-side library for Distributed Genome Annotation System
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 01 Sep 2005 13:10:39
Also Listed In: perl5
License: not specified in port
p5-Bio-Das-Lite 2.11 search for ports that depend on this port
Perl extension for the DAS (HTTP+XML) Protocol
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 01 Mar 2010 09:16:56
Also Listed In: perl5
License: ART10 GPLv1
p5-Bio-GFF3 2.0_1 search for ports that depend on this port
Fast low-level functions for parsing and formatting GFF3
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Apr 2011 08:51:49
Also Listed In: perl5
License: ART10 GPLv1
p5-Bio-Glite 0.10_1 search for ports that depend on this port
Perl Interface to G-language
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 02 Apr 2009 18:25:38
Also Listed In: perl5
License: not specified in port
p5-Bio-Graphics 2.38 search for ports that depend on this port
Generate GD Images of Bio::Seq Objects
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Mar 2009 18:52:27
Also Listed In: perl5
License: ART10 GPLv1
p5-Bio-MAGETAB 1.31 search for ports that depend on this port
Data model and utility API for the MAGE-TAB format
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 01 Jul 2009 09:03:56
Also Listed In: perl5
License: GPLv2
p5-Bio-NEXUS 0.78 search for ports that depend on this port
Object-oriented Perl API for the NEXUS file format
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Aug 2009 20:40:26
Also Listed In: perl5
License: not specified in port
p5-Bio-Phylo 0.56 search for ports that depend on this port
Phylogenetic analysis using Perl
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 13 May 2006 16:50:16
Also Listed In: perl5
License: ART10 GPLv1
p5-Bio-SCF 1.03 search for ports that depend on this port
Read and Update SCF Chromatographic Sequence Files
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Aug 2009 23:38:55
Also Listed In: perl5
License: not specified in port
p5-bioperl 1.6.924 search for ports that depend on this port
Collection of Perl modules for bioinformatics
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Jul 2000 11:06:03
Also Listed In: perl5
License: ART10 GPLv1
p5-bioperl-run 1.6.901 search for ports that depend on this port
Wrapper modules for common bioinformatics tools

There is no maintainer for this port.
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Port Added: 02 May 2006 21:32:38
Also Listed In: perl5
License: ART10 GPLv3
paml 4.8 search for ports that depend on this port
Phylogenetic Analysis by Maximum Likelihood (PAML)

There is no maintainer for this port.
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Port Added: 10 Jul 2000 00:21:06
License: not specified in port
phrap 1.090518 search for ports that depend on this port
Ignore IGNORE: you must request the source code \(distrib.tar.gz\) via e-mail, place it manually in /usr/local/PORTS-head/distfiles/phrap, and then try it again
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Phrap is a program for assembling shotgun DNA sequence data
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 24 May 2008 07:03:43
License: not specified in port
phred 0.020425.c search for ports that depend on this port
Restricted RESTRICTED: Redistribution is not permitted in any form. You must request the tarball via e-mail. Free for academic use.
Base calling and quality value assignment on DNA sequencing
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 24 May 2008 07:05:09
License: not specified in port
phylip 3.695_3,1 search for ports that depend on this port
Phylogeny Inference Package

There is no maintainer for this port.
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Port Added: 10 Jul 2000 00:25:48
License: not specified in port
phyml 20121109 search for ports that depend on this port
Simple, fast, and accurate algorithm to estimate large phylogenies

There is no maintainer for this port.
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Port Added: 21 Jul 2009 01:10:33
License: GPLv2
platon 2014.07.13_1 search for ports that depend on this port
Restricted RESTRICTED: free for academic, US5000 for commercial users
Tool for viewing molecular/crystallographic structures

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Port Added: unknown
License: not specified in port
plink 1.07_4 search for ports that depend on this port
Whole genome association analysis toolset
Maintained by: jwbacon@tds.net search for ports maintained by this maintainer
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2
plinkseq 0.08_2 search for ports that depend on this port
Toolset for working with human genetic variation data
Maintained by: jwbacon@tds.net search for ports maintained by this maintainer
Port Added: 27 Sep 2012 10:00:09
Also Listed In: science
License: GPLv2
povchem 1.0_7 search for ports that depend on this port
Simple yet powerful tool to generate POV from a PDB file

There is no maintainer for this port.
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Port Added: unknown
Also Listed In: graphics
License: not specified in port
primer3 2.3.6 search for ports that depend on this port
Primer3 helps to choose primers for PCR reactions

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Port Added: 17 Sep 2002 15:31:31
License: GPLv2
protomol 2.0.3_10 search for ports that depend on this port
OO, component based, framework for molecular dynamics (MD) simulations

There is no maintainer for this port.
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Port Added: 05 May 2006 20:12:57
License: not specified in port
psi88 1.0_7 search for ports that depend on this port
Plotting wavefunctions (molecular orbitals) in 3D

There is no maintainer for this port.
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Port Added: unknown
License: not specified in port
py-biopython 1.60_4 search for ports that depend on this port
Collection of Python modules for bioinformatics
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 31 Jul 2000 09:12:24
Also Listed In: python
License: not specified in port
pycogent 1.5.3_3 search for ports that depend on this port
Toolkit for statistical analysis of biological sequences
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Jun 2009 12:47:26
Also Listed In: python
License: GPLv2
pyfasta 0.5.2_1 search for ports that depend on this port
Fast, memory-efficient, pythonic access to fasta sequence files
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 18 Nov 2009 05:53:48
Also Listed In: python
License: MIT
python-nexus 0.87_1 search for ports that depend on this port
Generic nexus file format reader for python
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 29 Dec 2009 13:39:49
Also Listed In: python
License: not specified in port
raster3d 3.0.2_6* search for ports that depend on this port
Set of tools for generating raster images of proteins and molecules

There is no maintainer for this port.
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Port Added: 28 Apr 2006 14:21:11
Also Listed In: graphics
License: ART20
recombine 1.41 search for ports that depend on this port
Program to fit population models across sites

There is no maintainer for this port.
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Port Added: 06 Aug 2001 11:49:53
License: not specified in port
ruby-bio 1.4.1 search for ports that depend on this port
Integrated environment for Bioinformatics written in Ruby
Maintained by: mauricio@arareko.net search for ports maintained by this maintainer
Port Added: 24 Oct 2001 03:21:52
Also Listed In: ruby
License: not specified in port
seaview 4.5.2_1,1 search for ports that depend on this port
Multiple DNA/protein sequence alignment editor
Maintained by: 5u623l20@gmail.com search for ports maintained by this maintainer
Port Added: unknown
License: not specified in port
seqan 1.3.1_3 search for ports that depend on this port
C++ Sequence Analysis Library
Maintained by: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 06 Jun 2012 17:52:27
License: BSD3CLAUSE GPLv3
seqio 1.2.2_1 search for ports that depend on this port
Set of C functions which can read/write biological sequence files

There is no maintainer for this port.
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Port Added: 22 Aug 2001 09:07:26
License: not specified in port
seqtools 4.28 search for ports that depend on this port
Tools for visualising sequence alignments
Maintained by: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Nov 2013 11:01:14
License: GPLv3
sim4 2003.09.21_1 search for ports that depend on this port
Algorithm for aligning expressed DNA with genomic sequences

There is no maintainer for this port.
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Port Added: 27 Jul 2000 11:33:01
License: GPLv2
ssaha 3.1c_2 search for ports that depend on this port
Very fast matching and alignment of DNA sequences

There is no maintainer for this port.
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Port Added: 21 Jun 2008 00:02:14
License: not specified in port
tRNAscan-SE 1.23_1 search for ports that depend on this port
Improved tool for transfer RNA detection

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Port Added: 27 Mar 2002 14:19:04
License: not specified in port
t_coffee 9.03_3 search for ports that depend on this port
Multiple DNA or protein sequence alignment package

There is no maintainer for this port.
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Port Added: 25 Jan 2002 11:58:16
License: GPLv2
tinker 6.2.6_6 search for ports that depend on this port
Restricted RESTRICTED: author requests no distribution except from his FTP site
General purpose molecular modelling package

There is no maintainer for this port.
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Port Added: unknown
License: tinker
treepuzzle 5.2 search for ports that depend on this port
Maximum likelihood phylogeny reconstruction using quartets
Maintained by: jan.lentfer@web.de search for ports maintained by this maintainer
Port Added: 20 Nov 2002 09:04:07
License: not specified in port
treeviewx 0.5.1s20100823_1 search for ports that depend on this port
Phylogenetic tree viewer

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 17 Aug 2001 05:39:29
License: not specified in port
ugene 1.14.0_1 search for ports that depend on this port
Free, open-source, cross-platform bioinformatics toolkit
Maintained by: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 23 Feb 2013 04:51:12
Also Listed In: science
License: GPLv2
velvet 1.2.10_1 search for ports that depend on this port
Sequence assembler for very short reads
Maintained by: mzaki@m.u-tokyo.ac.jp search for ports maintained by this maintainer
Port Added: 07 Nov 2009 01:24:24
License: not specified in port
wise 2.4.1 search for ports that depend on this port
Intelligent algorithms for DNA searches

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Sep 2002 13:59:05
License: not specified in port
xmolwt 0.7_6 search for ports that depend on this port
Calculate atom weight and percent of each element for a given formula

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: unknown
License: not specified in port

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