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* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryRong-En Fan2008-04-061-0/+1
| | | | | | | | | | | | | | | | | | | | | 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> Notes: svn path=/head/; revision=210625
* MrBayes is a program for the Bayesian estimation of phylogeny.Martin Wilke2007-12-151-0/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=203737
* MUMmer is a modular system for the rapid whole genome alignment of finishedMartin Wilke2007-12-141-0/+1
| | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=203638
* - Sort category MakefilesAndrew Pantyukhin2007-10-051-2/+2
| | | | | | | | Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles Notes: svn path=/head/; revision=200970
* Remove expired leaf port:Vasil Dimov2007-01-251-1/+0
| | | | | | | | | | | | 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. Notes: svn path=/head/; revision=183249
* The BioCocoa framework provides developers with the opportunity to addDirk Meyer2006-12-301-0/+1
| | | | | | | | | | | | 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/ Notes: svn path=/head/; revision=181036
* Adun is a new extendible molecular simulation program that alsoDirk Meyer2006-11-091-0/+1
| | | | | | | | | | | includes data management and analysis capabilities. WWW: http://diana.imim.es/Adun Submitted by: Gürkan Sengün Reviewed by: dinoex Notes: svn path=/head/; revision=176957
* Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNACheng-Lung Sung2006-09-291-0/+1
| | | | | | | | | | and EST Sequences. PR: ports/103651 Submitted by: Bob Zimmermann <rpz at cse.wustl.edu> Notes: svn path=/head/; revision=174086
* Folding@Home is a distributed computing project -- people from through out thePav Lucistnik2006-08-281-0/+1
| | | | | | | | | | | | | | | | | 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> Notes: svn path=/head/; revision=171590
* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedPav Lucistnik2006-06-191-0/+1
| | | | | | | | | | | | | | | 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/ Notes: svn path=/head/; revision=165801
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.Aaron Dalton2006-05-131-0/+1
| | | | | | | Approved by: tobez (implicit) Notes: svn path=/head/; revision=162248
* Add protomol 2.0.3, OO, component based, framework for molecularEmanuel Haupt2006-05-051-0/+1
| | | | | | | | | | dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> Notes: svn path=/head/; revision=161442
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-021-0/+1
| | | | | | | | | | | | | 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> Notes: svn path=/head/; revision=161215
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-021-0/+1
| | | | | | | | | | | | | 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> Notes: svn path=/head/; revision=161213
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofRenato Botelho2006-03-161-0/+1
| | | | | | | | | | genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157464
* Add mafft 5.734, multiple sequence alignments based on fast FourierRenato Botelho2006-03-151-0/+1
| | | | | | | | | | transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157209
* Add dotter 20021204 # last modified date in FTP server, a viewer forRenato Botelho2006-03-151-0/+1
| | | | | | | | | | multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157195
* Add blat 33, a fast tool for local sequence similarity searches.Renato Botelho2006-03-151-0/+1
| | | | | | | | PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157190
* Add belvu 2.29, a viewer for multiple sequence alignments.Renato Botelho2006-03-151-0/+1
| | | | | | | | PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=157188
* Jalview is a multiple alignment editor written in Java. It is used widely in aHerve Quiroz2006-02-131-0/+1
| | | | | | | | | | | | | 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> Notes: svn path=/head/; revision=155905
* - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoidAlexey Dokuchaev2006-01-191-0/+1
| | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=153895
* - Remove expired portsPav Lucistnik2006-01-141-3/+0
| | | | Notes: svn path=/head/; revision=153501
* - Re-add p5-bioperl-devel, development version of biology/p5-bioperlSimon Barner2005-12-021-0/+1
| | | | | | | | | | (A collection of Perl modules for bioinformatics) PR: ports/89497 Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com> Notes: svn path=/head/; revision=150267
* Remove expired portsKris Kennaway2005-11-051-1/+0
| | | | Notes: svn path=/head/; revision=147349
* Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser forEmanuel Haupt2005-10-151-0/+1
| | | | | | | | | | | NCBI Entrez Gene. PR: 87423 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Approved by: novel (mentor) (implicit) Notes: svn path=/head/; revision=145476
* Add p5-Bio-Das 1.02, client-side library for Distributed GenomeRenato Botelho2005-09-011-0/+1
| | | | | | | | | | Annotation System. PR: ports/76379 Submitted by: Razi Khaja <razi@genet.sickkids.on.ca> Notes: svn path=/head/; revision=141702
* - biology/act is redundant after biology/artemis updateSergey Matveychuk2005-03-121-1/+0
| | | | | | | | | PR: ports/76217 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: maintainer timeout (2 monthes) Notes: svn path=/head/; revision=130960
* Add finchtv 1.3.0, a chromatogram trace viewer.Thierry Thomas2005-03-111-0/+1
| | | | | | | | PR: 70271 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> Notes: svn path=/head/; revision=130938
* As previously announced, remove ports that have reached their expiry date,Kris Kennaway2005-02-181-1/+0
| | | | | | | and the handful of ports that depended on them. Notes: svn path=/head/; revision=129234
* [new port] biology/embassySergey Matveychuk2004-11-261-0/+1
| | | | | | | | PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar> Notes: svn path=/head/; revision=122510
* Add blast, a powerful software package for gene and protein identification,Pav Lucistnik2004-11-111-0/+1
| | | | | | | | | | | 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> Notes: svn path=/head/; revision=121414
* Add ariadne 1.3, programs to compare protein sequences andKirill Ponomarev2004-06-221-0/+1
| | | | | | | | | | profiles, using the Smith-Waterman algorithm. PR: ports/67811 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Notes: svn path=/head/; revision=111985
* Remove category pkg/COMMENT files in favour of a COMMENT variable in theKris Kennaway2004-04-021-0/+2
| | | | | | | | | | category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651 Notes: svn path=/head/; revision=105948
* new port:biology/lsysexpEdwin Groothuis2003-09-031-0/+1
| | | | | | | | | | | | | | | | | | | | | 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> Notes: svn path=/head/; revision=88397
* As announced on May 6, remove the broken p5-bioperl-devel port.Kris Kennaway2003-08-081-1/+0
| | | | Notes: svn path=/head/; revision=86539
* A new port garlic, free molecular viewer and editor, free molecularMaho Nakata2003-07-281-0/+1
| | | | | | | | visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule. Notes: svn path=/head/; revision=85720
* Remove gaussian98Kris Kennaway2003-02-051-1/+0
| | | | | | | Pointy hat to: maho Notes: svn path=/head/; revision=74811
* New Port: biology/actEdwin Groothuis2003-01-161-0/+1
| | | | | | | | PR: ports/35753 Submitted by: Camson Huynh <chuynh@biolateral.com.au> Notes: svn path=/head/; revision=73258
* add treepuzzle 5.1Ying-Chieh Liao2002-11-201-0/+1
| | | | | | | | | | Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de> Notes: svn path=/head/; revision=70552
* Connect distribfold to build after moving it from misc categoryMario Sergio Fujikawa Ferreira2002-10-071-0/+1
| | | | | | | | | | Prompted by: kris, Adam Weinberger <adam@vectors.cx>, Fernan Aguero <fernan@iib.unsam.edu.ar>, others Notes: svn path=/head/; revision=67526
* add primer3 0.9Ying-Chieh Liao2002-09-171-0/+1
| | | | | | | | | | Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=66513
* Flip is used to find/translate orfs.Dirk Meyer2002-09-101-0/+1
| | | | | | | | | WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au Notes: svn path=/head/; revision=66055
* "Wise2 is package that is focused on comparing DNA sequences atDirk Meyer2002-09-101-0/+1
| | | | | | | | the level of its conceptual translation, regardless of sequencing error and introns." Notes: svn path=/head/; revision=66053
* New port L-Breeder version 1.0: Allows you to display and breedMario Sergio Fujikawa Ferreira2002-08-211-0/+1
| | | | | | | | | | L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com> Notes: svn path=/head/; revision=64720
* Add pymol 0.82, Free and Open-Source molecular modeling system.Hye-Shik Chang2002-08-131-0/+1
| | | | | | | | PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> Notes: svn path=/head/; revision=64463
* add libgenome 0.5.0Ying-Chieh Liao2002-07-301-0/+1
| | | | | | | Toolkit for developing bioinformatic related software in C++ Notes: svn path=/head/; revision=63725
* add avida 1.6.0Ying-Chieh Liao2002-04-201-0/+1
| | | | | | | | | | Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca> Notes: svn path=/head/; revision=57919
* Swiss-PdbViewer is an application that provides a user friendly interfaceDirk Meyer2002-04-021-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=57214
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.Johann Visagie2002-03-271-0/+1
| | | | | | | | PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au> Notes: svn path=/head/; revision=56744
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.Johann Visagie2002-03-271-0/+1
| | | | | | | | PR: 33853 Submitted by: chuynh@biolateral.com.au Notes: svn path=/head/; revision=56741
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