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Default branch: MAIN

Revision 1.120: download - view: text, markup, annotated - select for diffs
Mon Aug 1 04:29:37 2011 UTC (6 months, 1 week ago) by bapt
Branches: MAIN
CVS tags: RELEASE_9_0_0, HEAD
Diff to: previous 1.119: preferred, colored
Changes since revision 1.119: +0 -5 lines
Bye bye abandonwares (part 2)

2011-08-01 benchmarks/rawio: Looks like an abandonware, no more public distfiles
2011-08-01 benchmarks/tmetric: Looks like abandonware, no more public distfiles
2011-08-01 biology/L-Breeder: Looks like an abandonware, no more public distfile
2011-08-01 biology/crimap: Looks like an abandonware, no more public distfile
2011-08-01 biology/distribfold: No more upstream, looks like an abandonware
2011-08-01 biology/kinemage: Looks like an abandonware, no more public distfile
2011-08-01 biology/lsysexp: Looks like an abandonware, no more public distfile
2011-08-01 chinese/chm2html: Looks like an abandonware, no more public distfile
2011-08-01 chinese/ntuttf: No more public distfiles available
2011-08-01 chinese/reciteword: Looks like an abandonware, no more public distfile
2011-08-01 chinese/tocps: No more pulic distfiles
2011-08-01 chinese/xttmgr: Looks like an abandonware, no more public distfile
2011-08-01 comms/mserver: Looks like an abandonware, no more public distfiles
2011-08-01 comms/qicosi: Looks like an abandonware, no more public distfile
2011-08-01 comms/sms_client: Looks like an abandonware, no more public distfile
2011-08-01 comms/smstools: Looks like an abandonware, no more public distfile
2011-08-01 converters/siconv: Looks like an abandonware, no more public distfiles
2011-08-01 converters/utf8conv: Looks like an abandonware, no more public distfile
2011-08-01 databases/pgcluster: Looks like an abandonware, no more public distfile
2011-08-01 databases/py-MySQL: Please use databases/py-MySQLdb instead
2011-08-01 databases/py-SQLDict: Looks like an abandonware, no more public distfile
2011-08-01 databases/py-rrdpipe: Looks like an abandonware, no more public distfile
2011-08-01 databases/sybase_ase: no more public distfiles available
Revision 1.119: download - view: text, markup, annotated - select for diffs
Fri Apr 22 08:51:24 2011 UTC (9 months, 2 weeks ago) by wen
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Diff to: previous 1.118: preferred, colored
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Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.
All they do is convert back and forth between low-level Perl data
structures and GFF3 text.

WWW: http://search.cpan.org/dist/Bio-GFF3/
Revision 1.118: download - view: text, markup, annotated - select for diffs
Mon Mar 1 09:16:25 2010 UTC (23 months, 1 week ago) by wen
Branches: MAIN
CVS tags: RELEASE_8_2_0, RELEASE_8_1_0, RELEASE_7_4_0, RELEASE_7_3_0, RELEASE_6_EOL
Diff to: previous 1.117: preferred, colored
Changes since revision 1.117: +1 -0 lines
p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML
over HTTP primarily for biological-data).

WWW: http://search.cpan.org/dist/Bio-Das-Lite/

Feature safe:	yes
Revision 1.117: download - view: text, markup, annotated - select for diffs
Tue Dec 29 13:39:14 2009 UTC (2 years, 1 month ago) by wen
Branches: MAIN
Diff to: previous 1.116: preferred, colored
Changes since revision 1.116: +1 -0 lines
python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)
reader for python.

WWW:    http://simon.net.nz/articles/python-nexus
Revision 1.116: download - view: text, markup, annotated - select for diffs
Wed Nov 18 05:53:16 2009 UTC (2 years, 2 months ago) by wen
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Diff to: previous 1.115: preferred, colored
Changes since revision 1.115: +1 -0 lines
pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.

WWW:    http://bitbucket.org/brentp/biostuff/src/
Revision 1.115: download - view: text, markup, annotated - select for diffs
Sat Nov 7 01:23:58 2009 UTC (2 years, 3 months ago) by amdmi3
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Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

WWW: http://www.ebi.ac.uk/~zerbino/velvet/

PR:		140147
Submitted by:	Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
Revision 1.114: download - view: text, markup, annotated - select for diffs
Fri Aug 28 23:36:08 2009 UTC (2 years, 5 months ago) by miwi
Branches: MAIN
CVS tags: RELEASE_8_0_0
Diff to: previous 1.113: preferred, colored
Changes since revision 1.113: +1 -0 lines
Bio::SCF module allows you to read and update (in a restricted
way) SCF chromatographic sequence files. It is an interface to
Roger Staden's io-lib. See the installation directions for further
instructions.

WWW:	http://search.cpan.org/dist/Bio-SCF/

PR:		ports/138263
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.113: download - view: text, markup, annotated - select for diffs
Fri Aug 28 23:34:19 2009 UTC (2 years, 5 months ago) by miwi
Branches: MAIN
Diff to: previous 1.112: preferred, colored
Changes since revision 1.112: +1 -0 lines
Io_lib is a library of file reading and writing code to provide a
general purpose trace file (and Experiment File) reading interface.
The programmer simply calls the (eg) read_reading to create a "Read"
C structure with the data loaded into memory. It has been compiled
and tested on a variety of unix systems, MacOS X and MS Windows.

WWW:	http://staden.sourceforge.net/

PR:		ports/138254
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.112: download - view: text, markup, annotated - select for diffs
Sat Aug 22 20:39:51 2009 UTC (2 years, 5 months ago) by miwi
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Diff to: previous 1.111: preferred, colored
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Bio::NEXUS package provides an object-oriented, Perl-based
applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on.  This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data).

WWW: http://search.cpan.org/dist/Bio-NEXUS/

PR:		ports/137983
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.111: download - view: text, markup, annotated - select for diffs
Tue Jul 21 01:10:12 2009 UTC (2 years, 6 months ago) by amdmi3
Branches: MAIN
Diff to: previous 1.110: preferred, colored
Changes since revision 1.110: +1 -0 lines
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:		136877
Submitted by:	Ben Allen <ben@sysadminschronicles.com>
Revision 1.110: download - view: text, markup, annotated - select for diffs
Wed Jul 1 09:03:28 2009 UTC (2 years, 7 months ago) by miwi
Branches: MAIN
Diff to: previous 1.109: preferred, colored
Changes since revision 1.109: +1 -0 lines
p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This
is a beta release. All functions have now been implemented and most
have test suites; the exceptions include the modules involved in
export of MAGE-TAB documents, which are still a little experimental in
nature. The API is mostly finalised (and fully documented), but some
details may yet change where necessary to improve usability.

WWW: http://search.cpan.org/dist/Bio-MAGETAB/

PR:		ports/136021
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.109: download - view: text, markup, annotated - select for diffs
Mon Jun 22 12:46:56 2009 UTC (2 years, 7 months ago) by miwi
Branches: MAIN
Diff to: previous 1.108: preferred, colored
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PyCogent is a software library for genomic biology. It is a fully integrated
and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.

WWW:	http://pycogent.sourceforge.net/

PR:		ports/135863
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.108: download - view: text, markup, annotated - select for diffs
Mon Jun 8 23:49:59 2009 UTC (2 years, 8 months ago) by jasone
Branches: MAIN
Diff to: previous 1.107: preferred, colored
Changes since revision 1.107: +1 -0 lines
Add the biology/crux port.
Revision 1.107: download - view: text, markup, annotated - select for diffs
Fri Jun 5 20:38:33 2009 UTC (2 years, 8 months ago) by miwi
Branches: MAIN
Diff to: previous 1.106: preferred, colored
Changes since revision 1.106: +0 -2 lines
2009-05-31 biology/p5-bioperl-devel: no longer under development
2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
Revision 1.106: download - view: text, markup, annotated - select for diffs
Thu May 28 23:36:10 2009 UTC (2 years, 8 months ago) by miwi
Branches: MAIN
Diff to: previous 1.105: preferred, colored
Changes since revision 1.105: +1 -0 lines
LibSBML is an open-source programming library to help you read, write,
manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:		ports/135022
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.105: download - view: text, markup, annotated - select for diffs
Thu Apr 2 18:24:59 2009 UTC (2 years, 10 months ago) by miwi
Branches: MAIN
CVS tags: RELEASE_7_2_0
Diff to: previous 1.104: preferred, colored
Changes since revision 1.104: +1 -0 lines
Bio::Glite is an interface to G-language Genome Analysis Environment
through its REST web service (http://www.g-language.org). This module
allows almost everything G-language GAE can do, without installing
all necessary tookits and modules.

Advantage of this module over the standard installation of
G-language GAE package is:
   1. Easy installation from CPAN
   2. Extremely light-weight (less than 1000 lines of code)
   3. Does not require much CPU/RAM (all calculation is done on
the cloud)

Disadvantages includes:
   1. Slower analysis speed
   2. Internet connection is required
   3. No other software interfaces such as the G-language Shell

WWW: http://search.cpan.org/dist/Bio-Glite/

PR:		ports/133273
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.104: download - view: text, markup, annotated - select for diffs
Tue Mar 10 18:50:49 2009 UTC (2 years, 11 months ago) by miwi
Branches: MAIN
Diff to: previous 1.103: preferred, colored
Changes since revision 1.103: +1 -0 lines
p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)
for DNA and protein sequences.

WWW: http://search.cpan.org/dist/Bio-Graphics/

PR:		ports/132088
Submitted by:	Wen Heping <wenheping at gmail.com>
Revision 1.103: download - view: text, markup, annotated - select for diffs
Thu Jul 24 12:17:11 2008 UTC (3 years, 6 months ago) by pav
Branches: MAIN
CVS tags: RELEASE_7_1_0, RELEASE_6_4_0
Diff to: previous 1.102: preferred, colored
Changes since revision 1.102: +0 -1 lines
- Delete biology/nab port after being marked DEPRECATED for three months

PR:		ports/125891
Submitted by:	M. L. Dodson <mldodson@comcast.net> (maintainer)
Revision 1.102: download - view: text, markup, annotated - select for diffs
Sat Jun 21 00:01:56 2008 UTC (3 years, 7 months ago) by lippe
Branches: MAIN
Diff to: previous 1.101: preferred, colored
Changes since revision 1.101: +1 -0 lines
SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.

WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/

PR:		ports/124525
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	gabor (mentor, implicit)
Revision 1.101: download - view: text, markup, annotated - select for diffs
Sat May 24 07:04:45 2008 UTC (3 years, 8 months ago) by edwin
Branches: MAIN
CVS tags: RELEASE_5_EOL
Diff to: previous 1.100: preferred, colored
Changes since revision 1.100: +1 -0 lines
New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Revision 1.100: download - view: text, markup, annotated - select for diffs
Sat May 24 07:03:23 2008 UTC (3 years, 8 months ago) by edwin
Branches: MAIN
Diff to: previous 1.99: preferred, colored
Changes since revision 1.99: +1 -0 lines
New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Revision 1.99: download - view: text, markup, annotated - select for diffs
Sat May 24 07:01:55 2008 UTC (3 years, 8 months ago) by edwin
Branches: MAIN
Diff to: previous 1.98: preferred, colored
Changes since revision 1.98: +1 -0 lines
New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Revision 1.98: download - view: text, markup, annotated - select for diffs
Sat May 24 07:00:36 2008 UTC (3 years, 8 months ago) by edwin
Branches: MAIN
Diff to: previous 1.97: preferred, colored
Changes since revision 1.97: +1 -0 lines
New port: biology/consed viewing and editing workbench for sequence
assembly

	Consed is a tool for viewing, editing, and finishing sequence assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Revision 1.97: download - view: text, markup, annotated - select for diffs
Wed May 14 14:07:00 2008 UTC (3 years, 8 months ago) by pav
Branches: MAIN
Diff to: previous 1.96: preferred, colored
Changes since revision 1.96: +1 -0 lines
NJplot is a tree drawing program able to draw any phylogenetic tree expressed
in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP
package). NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building methods.

The package contains the following programs:
njplot      - draw phylogenetic trees and interactively modify them
newicktops  - non-interactive version rendering into a PostScript file
newicktotxt - non-interactive version rendering into a text file
unrooted    - draw unrooted circular trees

If you use NJplot in a published work, please cite the following reference:

Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for
biological sequence banks. Biochimie, 78, 364-369.

WWW: http://pbil.univ-lyon1.fr/software/njplot.html

PR:		ports/118438
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Revision 1.96: download - view: text, markup, annotated - select for diffs
Wed May 14 13:51:49 2008 UTC (3 years, 8 months ago) by pav
Branches: MAIN
Diff to: previous 1.95: preferred, colored
Changes since revision 1.95: +1 -0 lines
MUSCLE is multiple alignment software for protein and nucleotide sequences.
The name stands for multiple sequence comparison by log-expectation.

A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.

Citation:

Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.

Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.

The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.

WWW: http://www.drive5.com/muscle/

PR:		ports/118460
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
Revision 1.95: download - view: text, markup, annotated - select for diffs
Sun Apr 6 04:49:05 2008 UTC (3 years, 10 months ago) by rafan
Branches: MAIN
Diff to: previous 1.94: preferred, colored
Changes since revision 1.94: +1 -0 lines
MAPMAKER/EXP is a linkage analysis package designed to help construct primary
linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP
performs full multipoint linkage analysis (simultaneous estimation of all
recombination fractions from the primary data) for dominant, recessive, and co-
dominant (e.g.  RFLP-like) markers.  MAPMAKER/EXP is an experimental-cross-only
successor to the original MAPMAKER program.

MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map
genes controlling polygenic quantitative traits in F2 intercrosses and BC1
backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL
can be found in the technical report (included with MAPMAKER/QTL).

WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/

PR:		ports/122452
Submitted by:	Tassilo Philipp <tphilipp at potion-studios.com>
Revision 1.94: download - view: text, markup, annotated - select for diffs
Sat Dec 15 15:13:40 2007 UTC (4 years, 1 month ago) by miwi
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Diff to: previous 1.93: preferred, colored
Changes since revision 1.93: +1 -0 lines
MrBayes is a program for the Bayesian estimation of phylogeny.

Bayesian inference of phylogeny is based upon a quantity called the
posterior probability distribution of trees, which is the probability of a
tree conditioned on the observations. The conditioning is accomplished
using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.

WWW: http://mrbayes.csit.fsu.edu/

PR:		ports/118542
Submitted by:	mzaki at biol.s.u-tokyo.ac.jp
Revision 1.93: download - view: text, markup, annotated - select for diffs
Fri Dec 14 20:54:47 2007 UTC (4 years, 1 month ago) by miwi
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Diff to: previous 1.92: preferred, colored
Changes since revision 1.92: +1 -0 lines
MUMmer is a modular system for the rapid whole genome alignment of finished
or draft sequence. This package provides an efficient suffix tree library,
seed-and-extend alignment, SNP detection, repeat detection, and
visualization tools.

WWW:	http://mummer.sourceforge.net/

PR:		ports/118142
Submitted by:	Tony Maher
Revision 1.92: download - view: text, markup, annotated - select for diffs
Fri Oct 5 23:33:23 2007 UTC (4 years, 4 months ago) by sat
Branches: MAIN
CVS tags: RELEASE_7_0_0, RELEASE_6_3_0
Diff to: previous 1.91: preferred, colored
Changes since revision 1.91: +2 -2 lines
- Sort category Makefiles

Inspired by:	Jason Harris <jharris@widomaker.com>
Howto:		http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
Revision 1.91: download - view: text, markup, annotated - select for diffs
Thu Jan 25 11:25:40 2007 UTC (5 years ago) by vd
Branches: MAIN
CVS tags: RELEASE_4_EOL, PRE_XORG_7
Diff to: previous 1.90: preferred, colored
Changes since revision 1.90: +0 -1 lines
Remove expired leaf port:
2007-01-07 biology/coalesce: distfile disappeared from homepage

Actually the software is still available at:
http://evolution.gs.washington.edu/lamarc/coalesce.html, but it is
not supported by the authors. Last version is from 1995 and
biology/fluctuate can be used instead.
Revision 1.90: download - view: text, markup, annotated - select for diffs
Sat Dec 30 09:20:54 2006 UTC (5 years, 1 month ago) by dinoex
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Diff to: previous 1.89: preferred, colored
Changes since revision 1.89: +1 -0 lines
The BioCocoa framework provides developers with the opportunity to add
support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
TNT files by writing only three lines of code.
The framework is written in Cocoa (Objective-C).

WWW: http://bioinformatics.org/biococoa/
Revision 1.89: download - view: text, markup, annotated - select for diffs
Thu Nov 9 20:16:53 2006 UTC (5 years, 3 months ago) by dinoex
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Diff to: previous 1.88: preferred, colored
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Adun is a new extendible molecular simulation program that also
includes data management and analysis capabilities.

WWW: http://diana.imim.es/Adun
Submitted by:	Gürkan Sengün
Reviewed by:	dinoex
Revision 1.88: download - view: text, markup, annotated - select for diffs
Fri Sep 29 04:05:55 2006 UTC (5 years, 4 months ago) by clsung
Branches: MAIN
CVS tags: RELEASE_6_2_0
Diff to: previous 1.87: preferred, colored
Changes since revision 1.87: +1 -0 lines
Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA
and EST Sequences.

PR:		ports/103651
Submitted by:	Bob Zimmermann <rpz at cse.wustl.edu>
Revision 1.87: download - view: text, markup, annotated - select for diffs
Mon Aug 28 22:33:45 2006 UTC (5 years, 5 months ago) by pav
Branches: MAIN
Diff to: previous 1.86: preferred, colored
Changes since revision 1.86: +1 -0 lines
Folding@Home is a distributed computing project -- people from through out the
world download and run software to band together to make one of the largest
supercomputers in the world. Every computer makes the project closer to our
goals.
Folding@Home uses novel computational methods coupled to distributed computing,
to simulate problems thousands to millions of times more challenging than
previously achieved.

WWW: http://folding.standford.edu

PR:		ports/101235
Submitted by:	Yonatan <onatan@gmail.com>
Revision 1.86: download - view: text, markup, annotated - select for diffs
Mon Jun 19 20:32:08 2006 UTC (5 years, 7 months ago) by pav
Branches: MAIN
Diff to: previous 1.85: preferred, colored
Changes since revision 1.85: +1 -0 lines
SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated
protein similarities that plays a key role in many bioinformatics methods. It
contains about all currently published protein sequences and is continuously
updated.

The computational effort for keeping SIMAP up-to-date is constantly increasing.
Please help to update SIMAP by calculating protein similarities on your
computer.

WWW: http://boinc.bio.wzw.tum.de/boincsimap/
Revision 1.85: download - view: text, markup, annotated - select for diffs
Sat May 13 16:48:15 2006 UTC (5 years, 9 months ago) by aaron
Branches: MAIN
Diff to: previous 1.84: preferred, colored
Changes since revision 1.84: +1 -0 lines
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.

Approved by:	tobez (implicit)
Revision 1.84: download - view: text, markup, annotated - select for diffs
Fri May 5 20:09:54 2006 UTC (5 years, 9 months ago) by ehaupt
Branches: MAIN
Diff to: previous 1.83: preferred, colored
Changes since revision 1.83: +1 -0 lines
Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.

PR:		95123
Submitted by:	Sangwoo Shim <sangwoos@gmail.com>
Revision 1.83: download - view: text, markup, annotated - select for diffs
Tue May 2 21:31:42 2006 UTC (5 years, 9 months ago) by garga
Branches: MAIN
Diff to: previous 1.82: preferred, colored
Changes since revision 1.82: +1 -0 lines
Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93675
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
Revision 1.82: download - view: text, markup, annotated - select for diffs
Tue May 2 21:30:08 2006 UTC (5 years, 9 months ago) by garga
Branches: MAIN
Diff to: previous 1.81: preferred, colored
Changes since revision 1.81: +1 -0 lines
Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93674
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
Revision 1.81: download - view: text, markup, annotated - select for diffs
Thu Mar 16 22:31:25 2006 UTC (5 years, 10 months ago) by garga
Branches: MAIN
Diff to: previous 1.80: preferred, colored
Changes since revision 1.80: +1 -0 lines
Add lagan 1.2, efficient tools for large-scale multiple alignments of
genomic DNA.

PR:		ports/93058
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.80: download - view: text, markup, annotated - select for diffs
Wed Mar 15 10:41:16 2006 UTC (5 years, 10 months ago) by garga
Branches: MAIN
Diff to: previous 1.79: preferred, colored
Changes since revision 1.79: +1 -0 lines
Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.79: download - view: text, markup, annotated - select for diffs
Wed Mar 15 10:35:24 2006 UTC (5 years, 10 months ago) by garga
Branches: MAIN
Diff to: previous 1.78: preferred, colored
Changes since revision 1.78: +1 -0 lines
Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.

PR:		ports/93055
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.78: download - view: text, markup, annotated - select for diffs
Wed Mar 15 10:26:11 2006 UTC (5 years, 10 months ago) by garga
Branches: MAIN
Diff to: previous 1.77: preferred, colored
Changes since revision 1.77: +1 -0 lines
Add blat 33, a fast tool for local sequence similarity searches.

PR:		ports/93060
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.77: download - view: text, markup, annotated - select for diffs
Wed Mar 15 10:24:57 2006 UTC (5 years, 10 months ago) by garga
Branches: MAIN
Diff to: previous 1.76: preferred, colored
Changes since revision 1.76: +1 -0 lines
Add belvu 2.29, a viewer for multiple sequence alignments.

PR:		ports/93056
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.76: download - view: text, markup, annotated - select for diffs
Mon Feb 13 09:42:12 2006 UTC (5 years, 11 months ago) by hq
Branches: MAIN
CVS tags: RELEASE_6_1_0, RELEASE_5_5_0
Diff to: previous 1.75: preferred, colored
Changes since revision 1.75: +1 -0 lines
Jalview is a multiple alignment editor written in Java. It is used widely in a
variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain
database) and is also available as a general purpose alignment editor.

WWW: http://www.jalview.org

PR:		93054
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.75: download - view: text, markup, annotated - select for diffs
Thu Jan 19 19:47:59 2006 UTC (6 years ago) by danfe
Branches: MAIN
Diff to: previous 1.74: preferred, colored
Changes since revision 1.74: +1 -0 lines
- Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid
  unnecessary PORTEPOCH bump)
- Update MASTER_SITES and WWW line, provide backup download site
- Come up with better port description
- Reset maintainer to ports@
- Uphold CXX and CXXFLAGS
- Clean up Makefile slightly
- Don't install yet another copy of GPL and texts in French
- Add SHA256 hash to distinfo
Revision 1.74: download - view: text, markup, annotated - select for diffs
Sat Jan 14 21:15:44 2006 UTC (6 years ago) by pav
Branches: MAIN
Diff to: previous 1.73: preferred, colored
Changes since revision 1.73: +0 -3 lines
- Remove expired ports
Revision 1.73: download - view: text, markup, annotated - select for diffs
Fri Dec 2 21:40:11 2005 UTC (6 years, 2 months ago) by barner
Branches: MAIN
Diff to: previous 1.72: preferred, colored
Changes since revision 1.72: +1 -0 lines
- Re-add p5-bioperl-devel, development version of biology/p5-bioperl
  (A collection of Perl modules for bioinformatics)

PR:		ports/89497
Submitted by:	Mauricio Herrera Cuadra <arareko@yahoo.com>
Revision 1.72: download - view: text, markup, annotated - select for diffs
Sat Nov 5 09:07:06 2005 UTC (6 years, 3 months ago) by kris
Branches: MAIN
Diff to: previous 1.71: preferred, colored
Changes since revision 1.71: +0 -1 lines
Remove expired ports
Revision 1.71: download - view: text, markup, annotated - select for diffs
Sat Oct 15 20:09:49 2005 UTC (6 years, 3 months ago) by ehaupt
Branches: MAIN
Diff to: previous 1.70: preferred, colored
Changes since revision 1.70: +1 -0 lines
Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for
NCBI Entrez Gene.

PR:		87423
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
Approved by:	novel (mentor) (implicit)
Revision 1.70: download - view: text, markup, annotated - select for diffs
Thu Sep 1 13:09:32 2005 UTC (6 years, 5 months ago) by garga
Branches: MAIN
Diff to: previous 1.69: preferred, colored
Changes since revision 1.69: +1 -0 lines
Add p5-Bio-Das 1.02, client-side library for Distributed Genome
Annotation System.

PR:		ports/76379
Submitted by:	Razi Khaja <razi@genet.sickkids.on.ca>
Revision 1.69: download - view: text, markup, annotated - select for diffs
Sat Mar 12 08:07:23 2005 UTC (6 years, 11 months ago) by sem
Branches: MAIN
CVS tags: RELEASE_6_0_0, RELEASE_5_4_0
Diff to: previous 1.68: preferred, colored
Changes since revision 1.68: +0 -1 lines
- biology/act is redundant after biology/artemis update

PR:             ports/76217
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>
Approved by:	maintainer timeout (2 monthes)
Revision 1.68: download - view: text, markup, annotated - select for diffs
Fri Mar 11 21:16:15 2005 UTC (6 years, 11 months ago) by thierry
Branches: MAIN
Diff to: previous 1.67: preferred, colored
Changes since revision 1.67: +1 -0 lines
Add finchtv 1.3.0, a chromatogram trace viewer.

PR:		70271
Submitted by:	Fernan Aguero <fernan (at) iib.unsam.edu.ar>
Revision 1.67: download - view: text, markup, annotated - select for diffs
Fri Feb 18 23:44:28 2005 UTC (6 years, 11 months ago) by kris
Branches: MAIN
Diff to: previous 1.66: preferred, colored
Changes since revision 1.66: +0 -1 lines
As previously announced, remove ports that have reached their expiry date,
and the handful of ports that depended on them.
Revision 1.66: download - view: text, markup, annotated - select for diffs
Fri Nov 26 16:34:21 2004 UTC (7 years, 2 months ago) by sem
Branches: MAIN
CVS tags: RELEASE_4_11_0
Diff to: previous 1.65: preferred, colored
Changes since revision 1.65: +1 -0 lines
[new port] biology/embassy

PR:		ports/74330
Submitted by:	Fernan Aguero <fernan(at)iib.unsam.edu.ar>
Revision 1.65: download - view: text, markup, annotated - select for diffs
Thu Nov 11 21:35:03 2004 UTC (7 years, 3 months ago) by pav
Branches: MAIN
Diff to: previous 1.64: preferred, colored
Changes since revision 1.64: +1 -0 lines
Add blast, a powerful software package for gene and protein identification,
using sensitive, selective and rapid similarity searches of protein and
nucleotide sequence databases.

PR:		ports/69636
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.64: download - view: text, markup, annotated - select for diffs
Tue Jun 22 14:29:58 2004 UTC (7 years, 7 months ago) by krion
Branches: MAIN
CVS tags: RELEASE_5_3_0
Diff to: previous 1.63: preferred, colored
Changes since revision 1.63: +1 -0 lines
Add ariadne 1.3, programs to compare protein sequences and
profiles, using the Smith-Waterman algorithm.

PR:		ports/67811
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>
Revision 1.63: download - view: text, markup, annotated - select for diffs
Fri Apr 2 07:29:32 2004 UTC (7 years, 10 months ago) by kris
Branches: MAIN
CVS tags: RELEASE_4_10_0
Diff to: previous 1.62: preferred, colored
Changes since revision 1.62: +2 -0 lines
Remove category pkg/COMMENT files in favour of a COMMENT variable in the
category makefile.

Submitted by:	Matthew Seaman <m.seaman@infracaninophile.co.uk>
PR:		59651
Revision 1.62: download - view: text, markup, annotated - select for diffs
Wed Sep 3 02:23:23 2003 UTC (8 years, 5 months ago) by edwin
Branches: MAIN
CVS tags: RELEASE_5_2_1, RELEASE_5_2_0, RELEASE_4_9_0
Diff to: previous 1.61: preferred, colored
Changes since revision 1.61: +1 -0 lines
new port:biology/lsysexp

	L-system Explorer is a program used for viewing and creating
	L-system fractals.

	The following features are supported:

	- Over 500 builtin L-systems, arranged into about 20 groups.
	- Ability to create and save custom L-systems and L-system groups.
	- Abilty to save images of L-systems (in PNG or JPEG format).
	- Multiple L-systems can be viewed at the same time.
	- Able to use custom colors and gradients.
	- Can also generate random gradients, or completely random colors.
	- Able to draw using lines, points, or a random combination of both.

PR:		iports/51400
Submitted by:	David Yeske <dyeske@yahoo.com>
Revision 1.61: download - view: text, markup, annotated - select for diffs
Fri Aug 8 03:31:11 2003 UTC (8 years, 6 months ago) by kris
Branches: MAIN
Diff to: previous 1.60: preferred, colored
Changes since revision 1.60: +0 -1 lines
As announced on May 6, remove the broken p5-bioperl-devel port.
Revision 1.60: download - view: text, markup, annotated - select for diffs
Mon Jul 28 06:38:37 2003 UTC (8 years, 6 months ago) by maho
Branches: MAIN
Diff to: previous 1.59: preferred, colored
Changes since revision 1.59: +1 -0 lines
A new port garlic, free molecular viewer and editor, free molecular
visualization program, protein structure, DNA structure, PDB,
molecular rendering, biological macromolecule.
Revision 1.59: download - view: text, markup, annotated - select for diffs
Wed Feb 5 09:01:06 2003 UTC (9 years ago) by kris
Branches: MAIN
CVS tags: RELEASE_5_1_0, RELEASE_4_8_0
Diff to: previous 1.58: preferred, colored
Changes since revision 1.58: +0 -1 lines
Remove gaussian98

Pointy hat to:	maho
Revision 1.58: download - view: text, markup, annotated - select for diffs
Thu Jan 16 14:22:58 2003 UTC (9 years ago) by edwin
Branches: MAIN
Diff to: previous 1.57: preferred, colored
Changes since revision 1.57: +1 -0 lines
New Port: biology/act

PR:		ports/35753
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
Revision 1.57: download - view: text, markup, annotated - select for diffs
Wed Nov 20 08:54:10 2002 UTC (9 years, 2 months ago) by ijliao
Branches: MAIN
CVS tags: RELEASE_5_0_0
Diff to: previous 1.56: preferred, colored
Changes since revision 1.56: +1 -0 lines
add treepuzzle 5.1
Maximum likelihood phylogeny reconstruction using quartets

PR:		45241
Submitted by:	Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
Revision 1.56: download - view: text, markup, annotated - select for diffs
Mon Oct 7 03:07:59 2002 UTC (9 years, 4 months ago) by lioux
Branches: MAIN
Diff to: previous 1.55: preferred, colored
Changes since revision 1.55: +1 -0 lines
Connect distribfold to build after moving it from misc category

Prompted by:	kris,
		Adam Weinberger <adam@vectors.cx>,
		Fernan Aguero <fernan@iib.unsam.edu.ar>,
		others
Revision 1.55: download - view: text, markup, annotated - select for diffs
Tue Sep 17 15:31:07 2002 UTC (9 years, 4 months ago) by ijliao
Branches: MAIN
CVS tags: RELEASE_4_7_0
Diff to: previous 1.54: preferred, colored
Changes since revision 1.54: +1 -0 lines
add primer3 0.9
Primer3 helps to choose primers for PCR reactions

PR:		35298
Submitted by:	Tony Maher <tonym@biolateral.com.au>
Revision 1.54: download - view: text, markup, annotated - select for diffs
Tue Sep 10 14:04:04 2002 UTC (9 years, 5 months ago) by dinoex
Branches: MAIN
Diff to: previous 1.53: preferred, colored
Changes since revision 1.53: +1 -0 lines
Flip is used to find/translate orfs.
WWW: ftp://megasun.bch.umontreal.ca/pub/flip/
PR:		35332
Submitted by:	tonym@biolateral.com.au
Revision 1.53: download - view: text, markup, annotated - select for diffs
Tue Sep 10 13:58:38 2002 UTC (9 years, 5 months ago) by dinoex
Branches: MAIN
Diff to: previous 1.52: preferred, colored
Changes since revision 1.52: +1 -0 lines
"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns."
Revision 1.52: download - view: text, markup, annotated - select for diffs
Wed Aug 21 00:01:58 2002 UTC (9 years, 5 months ago) by lioux
Branches: MAIN
Diff to: previous 1.51: preferred, colored
Changes since revision 1.51: +1 -0 lines
New port L-Breeder version 1.0: Allows you to display and breed
L-system forms

PR:		38725
Submitted by:	David Yeske <dyeske@yahoo.com>
Revision 1.51: download - view: text, markup, annotated - select for diffs
Tue Aug 13 11:53:43 2002 UTC (9 years, 6 months ago) by perky
Branches: MAIN
Diff to: previous 1.50: preferred, colored
Changes since revision 1.50: +1 -0 lines
Add pymol 0.82, Free and Open-Source molecular modeling system.

PR:		40694
Submitted by:	Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
Revision 1.50: download - view: text, markup, annotated - select for diffs
Tue Jul 30 10:57:05 2002 UTC (9 years, 6 months ago) by ijliao
Branches: MAIN
Diff to: previous 1.49: preferred, colored
Changes since revision 1.49: +1 -0 lines
add libgenome 0.5.0
Toolkit for developing bioinformatic related software in C++
Revision 1.49: download - view: text, markup, annotated - select for diffs
Sat Apr 20 15:17:43 2002 UTC (9 years, 9 months ago) by ijliao
Branches: MAIN
CVS tags: RELEASE_4_6_2, RELEASE_4_6_1, RELEASE_4_6_0
Diff to: previous 1.48: preferred, colored
Changes since revision 1.48: +1 -0 lines
add avida 1.6.0
Avida is an auto-adaptive genetic system designed for ALife research

PR:		37268
Submitted by:	Jeremy Karlson <karlj000@unbc.ca>
Revision 1.48: download - view: text, markup, annotated - select for diffs
Tue Apr 2 16:18:48 2002 UTC (9 years, 10 months ago) by dinoex
Branches: MAIN
Diff to: previous 1.47: preferred, colored
Changes since revision 1.47: +1 -0 lines
Swiss-PdbViewer is an application that provides a user friendly interface
allowing to analyse several proteins at the same time. The proteins can be
superimposed in order to deduce structural alignments and compare their
active sites or any other relevant parts. Amino acid mutations, H-bonds,
angles and distances between atoms are easy to obtain thanks to the
intuitive graphic and menu interface.

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated
homology modelling server developped at Glaxo Welcome Experimental Research
in Geneva. Working with these two programs greatly reduces the amount of work
necessary to generate models, as it is possible to thread a protein primary
sequence onto a 3D template and get an immediate feedback of how well the
threaded protein will be accepted by the reference structure before
submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various
tools to build into the density. In addition, various modelling tools are
integrated and command files for popular energy minimisation packages can be
generated.

Finally, as a special bonus, POV-Ray scenes can be generated from the
current view in order to make stunning ray-traced quality images.

WWW:  http://www.expasy.ch/spdbv/

PR:		33902
Submitted by:	chuynh@biolateral.com.au
Revision 1.47: download - view: text, markup, annotated - select for diffs
Wed Mar 27 14:42:54 2002 UTC (9 years, 10 months ago) by wjv
Branches: MAIN
CVS tags: RELEASE_5_0_DP1
Diff to: previous 1.46: preferred, colored
Changes since revision 1.46: +1 -0 lines
Add crimap 2.4, a tool for the creation of multilocus linkage maps.

PR:		35198
Submitted by:	Tony Maher <tonym@biolateral.com.au>
Revision 1.46: download - view: text, markup, annotated - select for diffs
Wed Mar 27 14:18:45 2002 UTC (9 years, 10 months ago) by wjv
Branches: MAIN
Diff to: previous 1.45: preferred, colored
Changes since revision 1.45: +1 -0 lines
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.

PR:		33853
Submitted by:	chuynh@biolateral.com.au
Revision 1.45: download - view: text, markup, annotated - select for diffs
Fri Jan 25 14:58:11 2002 UTC (10 years ago) by wjv
Branches: MAIN
Diff to: previous 1.44: preferred, colored
Changes since revision 1.44: +1 -0 lines
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.
Revision 1.44: download - view: text, markup, annotated - select for diffs
Sat Dec 22 14:39:37 2001 UTC (10 years, 1 month ago) by kevlo
Branches: MAIN
CVS tags: RELEASE_4_5_0
Diff to: previous 1.43: preferred, colored
Changes since revision 1.43: +1 -0 lines
Initial import of artemis 4.0

Artemis is a  DNA sequence viewer and annotation tool.

PR: 32914
Submitted by: Camson <chuynh@biolateral.com.au>
Revision 1.43: download - view: text, markup, annotated - select for diffs
Wed Dec 19 10:03:26 2001 UTC (10 years, 1 month ago) by petef
Branches: MAIN
Diff to: previous 1.42: preferred, colored
Changes since revision 1.42: +1 -0 lines
Add gff2ps 0.97b, converts gff-formated genomic data-sets to
PostScript.

PR:		32920
Submitted by:	Camson Huynh <chuynh@biolateral.com.au>
Revision 1.42: download - view: text, markup, annotated - select for diffs
Wed Dec 19 03:20:46 2001 UTC (10 years, 1 month ago) by petef
Branches: MAIN
Diff to: previous 1.41: preferred, colored
Changes since revision 1.41: +1 -0 lines
Add dna-qc 1993.07.26, a quality control algorithm for DNA
sequencing projects.

PR:		32998
Submitted by:	Tony Maher <tonym@biolateral.com.au>
Revision 1.41: download - view: text, markup, annotated - select for diffs
Wed Oct 24 06:21:51 2001 UTC (10 years, 3 months ago) by knu
Branches: MAIN
Diff to: previous 1.40: preferred, colored
Changes since revision 1.40: +2 -1 lines
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics
written in Ruby.
Revision 1.40: download - view: text, markup, annotated - select for diffs
Wed Sep 26 09:21:53 2001 UTC (10 years, 4 months ago) by wjv
Branches: MAIN
Diff to: previous 1.39: preferred, colored
Changes since revision 1.39: +2 -1 lines
Add nclever 4.0, a character-based version of NCBI's Entrez program.

PR:		30783
Submitted by:	Tony Maher <tonym@biolateral.com.au>
Revision 1.39: download - view: text, markup, annotated - select for diffs
Wed Aug 22 12:07:22 2001 UTC (10 years, 5 months ago) by wjv
Branches: MAIN
CVS tags: RELEASE_4_4_0
Diff to: previous 1.38: preferred, colored
Changes since revision 1.38: +2 -1 lines
Add seqio 1.2.2, a set of C functions which can read/write
biological sequence files.

PR:		29922
Submitted by:	Tony Maher <tonym@biolateral.com.au>
Revision 1.38: download - view: text, markup, annotated - select for diffs
Fri Aug 17 08:39:25 2001 UTC (10 years, 5 months ago) by wjv
Branches: MAIN
Diff to: previous 1.37: preferred, colored
Changes since revision 1.37: +2 -1 lines
Add treeviewx 0.1.1, a phylogenetic tree viewer.

PR:		29770
Submitted by:	Tony Maher <tonym@biolateral.com.au>
Revision 1.37: download - view: text, markup, annotated - select for diffs
Tue Aug 14 09:36:30 2001 UTC (10 years, 5 months ago) by wjv
Branches: MAIN
Diff to: previous 1.36: preferred, colored
Changes since revision 1.36: +2 -1 lines
Add p5-bioperl-devel 0.9.0,
a collection of Perl modules for
bioinformatics (developer's release).
Revision 1.36: download - view: text, markup, annotated - select for diffs
Tue Aug 7 08:17:54 2001 UTC (10 years, 6 months ago) by wjv
Branches: MAIN
Diff to: previous 1.35: preferred, colored
Changes since revision 1.35: +2 -1 lines
Add lamarc 2001.08.06,
a package of programs for computing
population parameters.
Revision 1.35: download - view: text, markup, annotated - select for diffs
Mon Aug 6 14:49:26 2001 UTC (10 years, 6 months ago) by wjv
Branches: MAIN
Diff to: previous 1.34: preferred, colored
Changes since revision 1.34: +2 -1 lines
Add recombine 1.40, a program to fit population models across sites.
Revision 1.34: download - view: text, markup, annotated - select for diffs
Mon Aug 6 14:45:31 2001 UTC (10 years, 6 months ago) by wjv
Branches: MAIN
Diff to: previous 1.33: preferred, colored
Changes since revision 1.33: +2 -1 lines
Add fluctuate 1.30, a program to fit population models.
Revision 1.33: download - view: text, markup, annotated - select for diffs
Mon Aug 6 14:41:37 2001 UTC (10 years, 6 months ago) by wjv
Branches: MAIN
Diff to: previous 1.32: preferred, colored
Changes since revision 1.32: +2 -1 lines
Add coalesce 1.50, a program to fit population models.
Revision 1.32: download - view: text, markup, annotated - select for diffs
Mon Aug 6 13:07:39 2001 UTC (10 years, 6 months ago) by wjv
Branches: MAIN
Diff to: previous 1.31: preferred, colored
Changes since revision 1.31: +2 -1 lines
Add migrate 1.2,
a program to estimate population sizes and
migration rates.
Revision 1.31: download - view: text, markup, annotated - select for diffs
Wed Jul 4 08:39:28 2001 UTC (10 years, 7 months ago) by wjv
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Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny
Software.

PR:		28541
Submitted by:	dbader@eece.unm.edu
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Wed Feb 28 02:46:44 2001 UTC (10 years, 11 months ago) by ijliao
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reimport biology/genpak
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Wed Feb 28 02:43:09 2001 UTC (10 years, 11 months ago) by ijliao
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module name conflict with print/gp, so remove it and I'll reimport it again
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Tue Feb 27 17:22:24 2001 UTC (10 years, 11 months ago) by ijliao
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add gp
GP is a set of small utilities to manipulate DNA sequences
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Sun Feb 11 16:28:59 2001 UTC (11 years ago) by jeh
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- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and
  protein sequence search programs
- FASTA3 updates only some of the elements of FASTA2, which is why I have
  submitted ports of both versions (as biology/fasta and biology/fasta3)

PR:		24716
Submitted by:	Johann Visagie <johann@egenetics.com>
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Sun Feb 11 16:24:17 2001 UTC (11 years ago) by jeh
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New port: biology/fasta, the FASTA2 suite of DNA and protein sequence
search tools

PR:		24715
Submitted by:	Johann Visagie <johann@egenetics.com>
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Sat Feb 10 19:38:17 2001 UTC (11 years ago) by sf
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add gaussian98, an ab-initio molecular orbital calculation program.

PR:             23577
Submitted by:   NAKATA, Maho <chat95@mbox.kyoto-inet.or.jp>
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Sun Oct 29 13:56:21 2000 UTC (11 years, 3 months ago) by jeh
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New Port: biology/ncbi-toolkit
National Center for Biotechnology Information (NCBI) Development Toolkit.

PR:		22388
Submitted by:	Tony Maher <tony.maher@ebioinformatics.com>
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Thu Oct 12 12:31:10 2000 UTC (11 years, 4 months ago) by jeh
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Initial import of fastDNAml Version 1.2.2

The faster variant of DNAML, makes phylogenetic trees using maximum likelihood

PR:		21931
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
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Tue Oct 10 11:13:49 2000 UTC (11 years, 4 months ago) by jeh
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Initial import of biology/biojava

PR:		21678
Submitted by:	Brad Chapman <chapmanb@arches.uga.edu>
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Tue Oct 10 02:56:57 2000 UTC (11 years, 4 months ago) by jeh
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This is nab (nucleic acid builder), a language for macromolecules

PR:		21585
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU>
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Mon Jul 31 19:13:53 2000 UTC (11 years, 6 months ago) by nbm
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Diff to: previous 1.19: preferred, colored
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Add emboss, the European Molecular Biology Open Software Suite

PR:		ports/20317
Submitted by:	Johann Visagie <johann@egenetics.com>
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Mon Jul 31 12:12:23 2000 UTC (11 years, 6 months ago) by nbm
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Add py-biopython, is a collection of Python packages and modules created
by the Biopython Project, intended to provide the basis for building
bioinformatics applications in the Python language.

PR:		ports/20260
Submitted by:	Johann Visagie <johann@egenetics.com>
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Fri Jul 28 14:05:59 2000 UTC (11 years, 6 months ago) by nbm
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Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics

PR:		ports/20252
Submitted by:	Johann Visagie <johann@egenetics.com>
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Fri Jul 28 13:16:05 2000 UTC (11 years, 6 months ago) by nbm
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Add p5-AcePerl, a perl interface to the ACEDB genome database system

PR:		ports/20223
Submitted by:	Johann Visagie <johann@egenetics.com>
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Thu Jul 27 14:32:50 2000 UTC (11 years, 6 months ago) by nbm
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Add sim4, an implementation of the sim4 algorithm for aligning expressed
DNA with genomic sequences

PR:		ports/20219
Submitted by:	Johann Visagie <johann@egenetics.com>
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Wed Jul 19 13:23:00 2000 UTC (11 years, 6 months ago) by alex
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CVS tags: RELEASE_4_1_0
Diff to: previous 1.14: preferred, colored
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Add xdrawchem 0.82 - a program for drawing molecules
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Mon Jul 10 03:26:57 2000 UTC (11 years, 7 months ago) by steve
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Diff to: previous 1.13: preferred, colored
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Activating the chemeq, clustalw, paml, and phylip ports.
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Mon Sep 6 20:09:12 1999 UTC (12 years, 5 months ago) by taoka
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CVS tags: RELEASE_4_0_0, RELEASE_3_5_0, RELEASE_3_4_0, RELEASE_3_3_0
Diff to: previous 1.12: preferred, colored
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Added gperiodic and xmolwt
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Wed Aug 25 04:47:53 1999 UTC (12 years, 5 months ago) by obrien
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Diff to: previous 1.11: preferred, colored
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Change Id->FreeBSD.
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Wed May 19 13:38:46 1999 UTC (12 years, 8 months ago) by taoka
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Diff to: previous 1.10: preferred, colored
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Added deft and ortep3
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Fri May 7 06:59:25 1999 UTC (12 years, 9 months ago) by taoka
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Diff to: previous 1.9: preferred, colored
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Add platon and molden
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Thu May 6 08:18:35 1999 UTC (12 years, 9 months ago) by taoka
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Add mopac and psi88 (Move mopac and psi88 from misc to biology)
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Tue Nov 17 04:54:28 1998 UTC (13 years, 2 months ago) by jkoshy
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CVS tags: RELEASE_3_1_0, RELEASE_2_2_8
Diff to: previous 1.7: preferred, colored
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Activate tinker.
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Sun Jul 12 23:30:50 1998 UTC (13 years, 7 months ago) by steve
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CVS tags: RELEASE_3_0_0, RELEASE_2_2_7
Diff to: previous 1.6: preferred, colored
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Turn on hmmer.
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Mon Mar 16 07:01:32 1998 UTC (13 years, 10 months ago) by vanilla
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CVS tags: RELEASE_2_2_6
Diff to: previous 1.5: preferred, colored
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Activate povchem.
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Thu Jan 29 17:25:59 1998 UTC (14 years ago) by jseger
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Activate kinemage
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Sun Dec 21 22:05:43 1997 UTC (14 years, 1 month ago) by vanilla
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Activate seaview.
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Sun Dec 21 21:58:57 1997 UTC (14 years, 1 month ago) by vanilla
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Activate babel.
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Mon Dec 15 17:47:41 1997 UTC (14 years, 1 month ago) by vanilla
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Activate rasmol.
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Sat Dec 13 05:54:24 1997 UTC (14 years, 2 months ago) by asami
Branches: BIOLOGY
CVS tags: ports_biology
Diff to: previous 1.1: preferred, colored
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The new ports category "biology" starts here today.  No Darwin
jokes please!
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Sat Dec 13 05:54:24 1997 UTC (14 years, 2 months ago) by asami
Branches: MAIN
Initial revision
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