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Change Id->FreeBSD.
1999-08-25 06:58:03 +02:00
# $FreeBSD$
The new ports category "biology" starts here today. No Darwin jokes please!
1997-12-13 06:54:24 +01:00
#
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
2004-04-02 09:29:48 +02:00
COMMENT = Biology
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>
2002-08-21 02:01:59 +02:00
SUBDIR += L-Breeder
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
2006-11-09 21:16:54 +01:00
SUBDIR += adun
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>
2004-06-22 16:29:59 +02:00
SUBDIR += ariadne
Initial import of artemis 4.0 Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au>
2001-12-22 15:39:40 +01:00
SUBDIR += artemis
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>
2002-04-20 17:17:46 +02:00
SUBDIR += avida
Activate babel.
1997-12-21 22:58:57 +01:00
SUBDIR += babel
Add belvu 2.29, a viewer for multiple sequence alignments. PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 11:24:57 +01:00
SUBDIR += belvu
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/
2006-12-30 10:20:54 +01:00
SUBDIR += biococoa
Initial import of biology/biojava PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu>
2000-10-10 13:14:03 +02:00
SUBDIR += biojava
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>
2004-11-11 22:35:04 +01:00
SUBDIR += blast
Add blat 33, a fast tool for local sequence similarity searches. PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 11:26:12 +01:00
SUBDIR += blat
- Sort category Makefiles Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
2007-10-06 01:33:27 +02:00
SUBDIR += boinc-simap
- 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
2006-01-19 20:47:59 +01:00
SUBDIR += chemeq
- Sort category Makefiles Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles
2007-10-06 01:33:27 +02:00
SUBDIR += clustalw
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>
2008-05-24 09:00:37 +02:00
SUBDIR += consed
Add crimap 2.4, a tool for the creation of multilocus linkage maps. PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au>
2002-03-27 15:42:56 +01:00
SUBDIR += crimap
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
2002-10-07 05:07:59 +02:00
SUBDIR += distribfold
Add dna-qc 1993.07.26, a quality control algorithm for DNA sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au>
2001-12-19 04:20:48 +01:00
SUBDIR += dna-qc
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>
2006-03-15 11:35:24 +01:00
SUBDIR += dotter
[new port] biology/embassy PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar>
2004-11-26 17:34:22 +01:00
SUBDIR += embassy
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-31 21:13:54 +02:00
SUBDIR += emboss
New port: biology/fasta, the FASTA2 suite of DNA and protein sequence search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com>
2001-02-11 17:24:18 +01:00
SUBDIR += fasta
- 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>
2001-02-11 17:28:59 +01:00
SUBDIR += fasta3
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>
2000-10-12 14:31:13 +02:00
SUBDIR += fastdnaml
Add finchtv 1.3.0, a chromatogram trace viewer. PR: 70271 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar>
2005-03-11 22:16:16 +01:00
SUBDIR += finchtv
Add fluctuate 1.30, a program to fit population models.
2001-08-06 16:45:39 +02:00
SUBDIR += fluctuate
A new port garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule.
2003-07-28 08:38:37 +02:00
SUBDIR += garlic
reimport biology/genpak
2001-02-28 03:46:51 +01:00
SUBDIR += genpak
Add gff2ps 0.97b, converts gff-formated genomic data-sets to PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au>
2001-12-19 11:03:26 +01:00
SUBDIR += gff2ps
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>
2006-09-29 06:05:55 +02:00
SUBDIR += gmap
Added gperiodic and xmolwt
1999-09-06 22:09:12 +02:00
SUBDIR += gperiodic
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny Software. PR: 28541 Submitted by: dbader@eece.unm.edu
2001-07-04 10:39:40 +02:00
SUBDIR += grappa
Turn on hmmer.
1998-07-13 01:30:50 +02:00
SUBDIR += hmmer
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>
2006-02-13 10:42:13 +01:00
SUBDIR += jalview
Activate kinemage
1998-01-29 18:25:59 +01:00
SUBDIR += kinemage
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>
2006-03-16 23:31:26 +01:00
SUBDIR += lagan
Add lamarc 2001.08.06, a package of programs for computing population parameters.
2001-08-07 10:17:58 +02:00
SUBDIR += lamarc
add libgenome 0.5.0 Toolkit for developing bioinformatic related software in C++
2002-07-30 12:57:06 +02:00
SUBDIR += libgenome
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>
2006-08-29 00:33:45 +02:00
SUBDIR += linux-foldingathome
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>
2003-09-03 04:23:23 +02:00
SUBDIR += lsysexp
Add mafft 5.734, multiple sequence alignments based on fast Fourier transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar>
2006-03-15 11:41:16 +01:00
SUBDIR += mafft
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>
2008-04-06 06:49:05 +02:00
SUBDIR += mapm3
Add migrate 1.2, a program to estimate population sizes and migration rates.
2001-08-06 15:07:46 +02:00
SUBDIR += migrate
Add platon and molden
1999-05-07 08:59:25 +02:00
SUBDIR += molden
Add mopac and psi88 (Move mopac and psi88 from misc to biology)
1999-05-06 10:18:35 +02:00
SUBDIR += mopac
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
2007-12-15 16:13:41 +01:00
SUBDIR += mrbayes
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
2007-12-14 21:54:47 +01:00
SUBDIR += mummer
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>
2008-05-14 15:51:50 +02:00
SUBDIR += muscle
This is nab (nucleic acid builder), a language for macromolecules PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU>
2000-10-10 04:56:57 +02:00
SUBDIR += nab
New Port: biology/ncbi-toolkit National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com>
2000-10-29 14:56:24 +01:00
SUBDIR += ncbi-toolkit
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>
2008-05-14 16:07:01 +02:00
SUBDIR += njplot
Added deft and ortep3
1999-05-19 15:38:46 +02:00
SUBDIR += ortep3
Add p5-AcePerl, a perl interface to the ACEDB genome database system PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-28 15:16:10 +02:00
SUBDIR += p5-AcePerl
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)
2005-10-15 22:09:50 +02:00
SUBDIR += p5-Bio-ASN1-EntrezGene
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>
2005-09-01 15:09:32 +02:00
SUBDIR += p5-Bio-Das
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. Approved by: tobez (implicit)
2006-05-13 18:48:15 +02:00
SUBDIR += p5-Bio-Phylo
Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com>
2000-07-28 16:06:03 +02:00
SUBDIR += p5-bioperl
- 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>
2005-12-02 22:40:12 +01:00
SUBDIR += p5-bioperl-devel
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>
2006-05-02 23:30:08 +02:00
SUBDIR += p5-bioperl-run
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>
2006-05-02 23:31:43 +02:00
SUBDIR += p5-bioperl-run-devel
Activating the chemeq, clustalw, paml, and phylip ports.
2000-07-10 05:26:57 +02:00
SUBDIR += paml
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>
2008-05-24 09:01:56 +02:00
SUBDIR += phd2fasta
Activating the chemeq, clustalw, paml, and phylip ports.
2000-07-10 05:26:57 +02:00
SUBDIR += phylip
Add platon and molden
1999-05-07 08:59:25 +02:00
SUBDIR += platon
Activate povchem.
1998-03-16 08:01:32 +01:00
SUBDIR += povchem
add primer3 0.9 Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au>
2002-09-17 17:31:09 +02:00
SUBDIR += primer3
Add protomol 2.0.3, OO, component based, framework for molecular dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com>
2006-05-05 22:09:54 +02:00
SUBDIR += protomol
Add mopac and psi88 (Move mopac and psi88 from misc to biology)
1999-05-06 10:18:35 +02:00
SUBDIR += psi88
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>
2000-07-31 14:12:24 +02:00
SUBDIR += py-biopython
Add pymol 0.82, Free and Open-Source molecular modeling system. PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
2002-08-13 13:53:43 +02:00
SUBDIR += pymol
Activate rasmol.
1997-12-15 18:47:41 +01:00
SUBDIR += rasmol
Add recombine 1.40, a program to fit population models across sites.
2001-08-06 16:49:53 +02:00
SUBDIR += recombine
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics written in Ruby.
2001-10-24 08:21:52 +02:00
SUBDIR += ruby-bio
Activate seaview.
1997-12-21 23:05:43 +01:00
SUBDIR += seaview
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>
2001-08-22 14:07:26 +02:00
SUBDIR += seqio
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>
2000-07-27 16:33:00 +02:00
SUBDIR += sim4
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. PR: 33853 Submitted by: chuynh@biolateral.com.au
2002-03-27 15:18:49 +01:00
SUBDIR += tRNAscan-SE
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.
2002-01-25 15:58:16 +01:00
SUBDIR += t_coffee
Activate tinker.
1998-11-17 05:54:28 +01:00
SUBDIR += tinker
add treepuzzle 5.1 Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de>
2002-11-20 09:54:10 +01:00
SUBDIR += treepuzzle
Add treeviewx 0.1.1, a phylogenetic tree viewer. PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au>
2001-08-17 10:39:28 +02:00
SUBDIR += treeviewx
"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns."
2002-09-10 15:58:40 +02:00
SUBDIR += wise
Add xdrawchem 0.82 - a program for drawing molecules
2000-07-19 15:23:02 +02:00
SUBDIR += xdrawchem
Added gperiodic and xmolwt
1999-09-06 22:09:12 +02:00
SUBDIR += xmolwt
The new ports category "biology" starts here today. No Darwin jokes please!
1997-12-13 06:54:24 +01:00
.include <bsd.port.subdir.mk>
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