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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: 92

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


Result Page: 1   Next
InsightToolkit Insight Toolkit
2.8.1_2* search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 07 Sep 2006 03:14:06
Also Listed In: science
License: not specified in port
afni Advanced Functional Neuro Imaging
2012.04.17.2129_11* search for ports that depend on this port
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 Programs to compare protein sequences and profiles
1.3 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 22 Jun 2004 14:31:00
License: not specified in port
artemis DNA sequence viewer and annotation tool
9_1 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 22 Dec 2001 11:39:40
Also Listed In: java
License: not specified in port
avida Auto-adaptive genetic system designed for ALife research
2.12.4 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 20 Apr 2002 15:17:56
License: GPLv3
babel Converts among various molecular file formats
1.6_4 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: unknown
Also Listed In: converters
License: not specified in port
biococoa Bioinformatics framework
2.2.2_1 search for ports that depend on this port
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 Open-source Java tools for processing biological data
1.7,1 search for ports that depend on this port
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 Fast tool for local sequence similarity searches
35 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 15 Mar 2006 10:29:12
License: not specified in port
boinc-simap Similarity Matrix of Proteins project for BOINC
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

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 Outputs LaTeX code for chemical reaction
1.50_2 search for ports that depend on this port

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

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 Graphical tool for editing Phrap assemblies
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.
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 Software toolkit for phylogenetic inference
1.2.0_5 search for ports that depend on this port

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Port Added: 08 Jun 2009 23:51:06
Also Listed In: python
License: BSD2CLAUSE BSD3CLAUSE
cycle Calendar program for women
0.3.1_9* search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 30 Jun 2005 14:05:46
Also Listed In: deskutils python
License: GPLv2
emboss Collection of open source tools for genetic sequence analysis
6.6.0 search for ports that depend on this port
Maintained by: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 31 Jul 2000 16:13:54
License: GPLv2
fasta Collection of programs for searching DNA and protein databases
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

There is no maintainer for this port.
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Port Added: 11 Feb 2001 13:24:20
License: not specified in port
fasta3 Collection of programs for searching DNA and protein databases
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

There is no maintainer for this port.
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Port Added: 11 Feb 2001 13:29:00
License: Fasta
fastdnaml Faster DNAML, makes phylogenetic trees using maximum likelihood
1.2.2_2 search for ports that depend on this port

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Port Added: 12 Oct 2000 09:31:14
License: GPLv2
fluctuate Program to fit population models
1.40 search for ports that depend on this port

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Port Added: 06 Aug 2001 11:45:39
License: not specified in port
garlic Molecular viewer, editor, and visualization program
1.6_1 search for ports that depend on this port
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 Converts gff-formated genomic data-sets to PostScript
0.98d_2 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 19 Dec 2001 07:03:28
License: GPLv2
gmap Genomic Mapping and Alignment Program for mRNA and EST Sequences
2006.04.21_1 search for ports that depend on this port
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 Displays a periodic table of the elements
2.0.10_7 search for ports that depend on this port

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Port Added: unknown
License: not specified in port
grappa Genome Rearrangements Analysis and Phylogeny Software
2.0 search for ports that depend on this port

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Port Added: 04 Jul 2001 05:39:40
License: not specified in port
hmmer Profile hidden Markov models for biological sequence analysis
3.0 search for ports that depend on this port

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Port Added: unknown
License: not specified in port
iolib General purpose trace file (and Experiment File) reading interface
1.13.7 search for ports that depend on this port
Maintained by: danilo@FreeBSD.org search for ports maintained by this maintainer
Port Added: 28 Aug 2009 23:34:46
License: BSD3CLAUSE
jalview Viewer and editor for multiple sequence alignments
2.07_2 search for ports that depend on this port

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Port Added: 13 Feb 2006 09:43:01
Also Listed In: java
License: not specified in port
lagan Efficient tools for large-scale multiple alignments of genomic DNA
2.0 search for ports that depend on this port

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Port Added: 16 Mar 2006 22:31:50
License: GPLv2
lamarc Package of programs for computing population parameters
2.1.8,1 search for ports that depend on this port

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Port Added: 07 Aug 2001 05:17:58
License: APACHE20
libsbml API Library for Working with SBML File
5.10.2 search for ports that depend on this port

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Port Added: 28 May 2009 23:36:42
Also Listed In: devel
License: LGPL21
linux-foldingathome Distributed client for Protein Folding
5.04 search for ports that depend on this port
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 Multiple alignment program for amino acid or nucleotide sequences
7.149 search for ports that depend on this port
Maintained by: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:41:45
License: BSD2CLAUSE
mapm3 Constructs linkage maps of markers segregating in experimental crosses
3.0 search for ports that depend on this port
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 Program to estimate population sizes and migration rates
3.5.1 search for ports that depend on this port
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 Medical Imaging NetCDF
2.2.00,1* search for ports that depend on this port

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Port Added: 30 Apr 2006 12:09:06
Also Listed In: science
License: BSD
molden Display molecular orbitals and electron densities in 2D and 3D
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.

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Port Added: unknown
License: not specified in port
mopac Semi-empirical (MNDO, etc.) molecular orbital calculation
7.1.11_4,1 search for ports that depend on this port

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Port Added: unknown
License: not specified in port
mrbayes Bayesian inference of phylogeny
3.1.2_1 search for ports that depend on this port
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 Modular system for rapid whole genome alignment
3.23_1 search for ports that depend on this port

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Port Added: 14 Dec 2007 20:56:11
License: not specified in port
muscle MUltiple Sequence Comparison by Log-Expectation
3.8.31 search for ports that depend on this port
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-blast NCBI implementation of Basic Local Alignment Search Tool
2.2.30 search for ports that depend on this port
Maintained by: jwbacon@tds.net search for ports maintained by this maintainer
Port Added: 06 Oct 2014 20:17:07
License: Public_domain
ncbi-toolkit NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
2012.06.20 search for ports that depend on this port

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Port Added: 29 Oct 2000 10:56:24
License: not specified in port
njplot Phylogenetic tree drawing program capable of interactive manipulation
2.1_3 search for ports that depend on this port
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 Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure
1.0.3_9 search for ports that depend on this port

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Port Added: unknown
License: not specified in port
p5-AcePerl Perl5 interface to the ACEDB genome database system
1.92_2 search for ports that depend on this port

There is no maintainer for this port.
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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 Regular expression-based Perl Parser for NCBI Entrez Gene
1.091 search for ports that depend on this port
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 Client-side library for Distributed Genome Annotation System
1.17_2 search for ports that depend on this port
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 Perl extension for the DAS (HTTP+XML) Protocol
2.11 search for ports that depend on this port
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 Fast low-level functions for parsing and formatting GFF3
2.0_1 search for ports that depend on this port
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 Perl Interface to G-language
0.10_1 search for ports that depend on this port
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 Generate GD Images of Bio::Seq Objects
2.38 search for ports that depend on this port
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 Data model and utility API for the MAGE-TAB format
1.31 search for ports that depend on this port
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 Object-oriented Perl API for the NEXUS file format
0.78 search for ports that depend on this port
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 Phylogenetic analysis using Perl
0.56 search for ports that depend on this port
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 Read and Update SCF Chromatographic Sequence Files
1.03 search for ports that depend on this port
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 Collection of Perl modules for bioinformatics
1.6.924 search for ports that depend on this port
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 Wrapper modules for common bioinformatics tools
1.6.901 search for ports that depend on this port

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Port Added: 02 May 2006 21:32:38
Also Listed In: perl5
License: ART10 GPLv3
paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.8 search for ports that depend on this port

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Port Added: 10 Jul 2000 00:21:06
License: not specified in port
phrap Phrap is a program for assembling shotgun DNA sequence data
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.
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 Base calling and quality value assignment on DNA sequencing
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.
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 Phylogeny Inference Package
3.695_3,1 search for ports that depend on this port

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 Simple, fast, and accurate algorithm to estimate large phylogenies
20121109 search for ports that depend on this port

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Port Added: 21 Jul 2009 01:10:33
License: GPLv2
platon Tool for viewing molecular/crystallographic structures
2014.07.13_1 search for ports that depend on this port
Restricted RESTRICTED: free for academic, US5000 for commercial users

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Port Added: unknown
License: not specified in port
plink Whole genome association analysis toolset
1.07_4 search for ports that depend on this port
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 Toolset for working with human genetic variation data
0.10 search for ports that depend on this port
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 Simple yet powerful tool to generate POV from a PDB file
1.0_7 search for ports that depend on this port

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Port Added: unknown
Also Listed In: graphics
License: not specified in port
primer3 Primer3 helps to choose primers for PCR reactions
2.3.6 search for ports that depend on this port

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

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Port Added: 05 May 2006 20:12:57
License: not specified in port
psi88 Plotting wavefunctions (molecular orbitals) in 3D
1.0_7 search for ports that depend on this port

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Port Added: unknown
License: not specified in port
py-biopython Collection of Python modules for bioinformatics
1.60_4 search for ports that depend on this port
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 Toolkit for statistical analysis of biological sequences
1.5.3_3 search for ports that depend on this port
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 Fast, memory-efficient, pythonic access to fasta sequence files
0.5.2_1 search for ports that depend on this port
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 Generic nexus file format reader for python
0.87_1 search for ports that depend on this port
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 Set of tools for generating raster images of proteins and molecules
3.0.2_6* search for ports that depend on this port

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 Program to fit population models across sites
1.41 search for ports that depend on this port

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Port Added: 06 Aug 2001 11:49:53
License: not specified in port
ruby-bio Integrated environment for Bioinformatics written in Ruby
1.4.1 search for ports that depend on this port
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 Multiple DNA/protein sequence alignment editor
4.5.2_1,1 search for ports that depend on this port
Maintained by: 5u623l20@gmail.com search for ports maintained by this maintainer
Port Added: unknown
License: not specified in port
seqan C++ Sequence Analysis Library
1.3.1_3 search for ports that depend on this port
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 Set of C functions which can read/write biological sequence files
1.2.2_1 search for ports that depend on this port

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 Tools for visualising sequence alignments
4.29 search for ports that depend on this port
Maintained by: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Nov 2013 11:01:14
License: GPLv3
sim4 Algorithm for aligning expressed DNA with genomic sequences
2003.09.21_1 search for ports that depend on this port

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

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Port Added: 21 Jun 2008 00:02:14
License: not specified in port
tRNAscan-SE Improved tool for transfer RNA detection
1.23_1 search for ports that depend on this port

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

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

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Port Added: unknown
License: tinker
treepuzzle Maximum likelihood phylogeny reconstruction using quartets
5.2 search for ports that depend on this port
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 Phylogenetic tree viewer
0.5.1s20100823_1 search for ports that depend on this port

There is no maintainer for this port.
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Port Added: 17 Aug 2001 05:39:29
License: not specified in port
ugene Free, open-source, cross-platform bioinformatics toolkit
1.14.2 search for ports that depend on this port
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 Sequence assembler for very short reads
1.2.10_1 search for ports that depend on this port
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 Intelligent algorithms for DNA searches
2.4.1 search for ports that depend on this port

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 Calculate atom weight and percent of each element for a given formula
0.7_6 search for ports that depend on this port

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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