kpriv/freebsd-ports
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity
freebsd-ports/biology/Makefile

105 lines
2.2 KiB
Makefile
Raw Normal View History

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
Add the biology/crux port.
2009-06-09 01:49:59 +02:00
SUBDIR += crux
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
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>
2009-08-29 01:34:20 +02:00
SUBDIR += iolib
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
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>
2009-05-29 01:36:10 +02:00
SUBDIR += libsbml
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
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
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>
2009-04-02 20:24:59 +02:00
SUBDIR += p5-Bio-Glite
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>
2009-03-10 19:50:49 +01:00
SUBDIR += p5-Bio-Graphics
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>
2009-07-01 11:03:28 +02:00
SUBDIR += p5-Bio-MAGETAB
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>
2009-08-22 22:39:51 +02:00
SUBDIR += p5-Bio-NEXUS
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
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>
2009-08-29 01:36:09 +02:00
SUBDIR += p5-Bio-SCF
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
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
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
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 09:03:23 +02:00
SUBDIR += phrap
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 09:04:45 +02:00
SUBDIR += phred
Activating the chemeq, clustalw, paml, and phylip ports.
2000-07-10 05:26:57 +02:00
SUBDIR += phylip
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>
2009-07-21 03:10:13 +02:00
SUBDIR += phyml
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
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>
2009-06-22 14:46:56 +02:00
SUBDIR += pycogent
pyfasta is a python module for fast, memory-efficient, pythonic access to fasta sequence files. WWW: http://bitbucket.org/brentp/biostuff/src/
2009-11-18 06:53:17 +01:00
SUBDIR += pyfasta
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
python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees) reader for python. WWW: http://simon.net.nz/articles/python-nexus
2009-12-29 14:39:14 +01:00
SUBDIR += python-nexus
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
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)
2008-06-21 02:01:57 +02:00
SUBDIR += ssaha
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
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>
2009-11-07 02:23:59 +01:00
SUBDIR += velvet
"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>
Reference in a new issue Copy permalink