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* [new port] biology/canu: Single molecule sequence assemblerjwb2017-12-221-0/+1
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adap...jwb2017-12-091-0/+1
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)...jwb2017-12-031-0/+1
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ...jwb2017-12-031-0/+1
* [new port] biology/fastqc: Quality control tool for high throughput sequence ...jwb2017-12-011-0/+1
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, pojwb2017-11-301-0/+1
* New port, biology/iqtree: Efficient phylogenomic softwarejrm2017-10-221-0/+1
* Add p5-Bio-FeatureIO 1.6.905sunpoet2017-09-161-0/+1
* Remove expired ports:rene2017-08-231-1/+0
* bx-python is a python library and associated set of scripts to allow for rapidmiwi2017-05-061-0/+1
* pysam is a lightweight wrapper of the htslib C-API and provides facilities tomiwi2017-05-061-0/+1
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (goog...ler2017-04-301-1/+0
* Move devel/rubygem-bio to biology/rubygem-biosunpoet2017-02-051-0/+1
* - Add p5-Bio-Coordinate 1.007001sunpoet2016-12-191-0/+1
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-Runsunpoet2016-12-181-1/+1
* - Move biology/p5-bioperl to biology/p5-BioPerlsunpoet2016-12-181-1/+1
* biology/njplot: Revive and update to version 2.4jrm2016-11-161-0/+1
* Remove expired ports without open PRs:rene2016-07-051-1/+0
* biology/seqan: update 1.3.1 -> 2.1.1junovitch2016-05-101-0/+1
* New port: biology/seqan-appsjunovitch2016-05-101-0/+1
* The BIOM file format (canonically pronounced biome) is designed to be aolivierd2016-05-101-0/+1
* DNA query sequences against a protein reference database (BLASTP and BLASTXwen2016-05-061-0/+1
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.amdmi32016-03-241-0/+1
* New port: biology/bowtie2.rakuco2016-03-231-0/+1
* New port: biology/slclust.rakuco2016-03-231-0/+1
* Trimmomatic performs a variety of useful trimming tasks for illuminawen2016-03-171-0/+1
* New port: biology/p5-transdecoderpi2016-03-171-0/+1
* New port: biology/bowtie.rakuco2016-03-051-0/+1
* New port: biology/vcftools.rakuco2016-02-271-0/+1
* The bedtools utilities are a suite of tools for performing a wide range ofwen2016-01-191-0/+1
* Remove expired ports:rene2015-11-291-3/+0
* BWA is a program for aligning sequencing reads against a large referencerm2015-09-261-0/+1
* Fast indexing and retrieval of FASTA records from flat file data bases.rm2015-09-261-0/+1
* Simple and quick FastQ and FastA tool for file reading and conversion.rm2015-09-261-0/+1
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromrm2015-09-261-0/+1
* The FASTX-Toolkit is a collection of command line tools for Short-Readsrm2015-09-261-0/+1
* Gordon's text utilities.rm2015-09-261-0/+1
* CD-HIT is a very widely used program for clustering and comparing protein orwen2015-09-191-0/+1
* New port: biology/bcftoolspi2015-06-061-0/+1
* Remove expired ports:rene2015-01-011-1/+0
* Rename biology/ncbi-blast to biology/ncbi-blast+grembo2014-12-311-1/+1
* Samtools implements various utilities for post-processing alignments in thepawel2014-12-161-0/+1
* HTSlib is an implementation of a unified C library for accessing common filepawel2014-12-151-0/+1
* Add new port biology/ncbi-blastmarino2014-10-071-0/+1
* Second run at cleaning out non staged ports without pending PRbapt2014-09-021-1/+0
* Remove non staged ports without pending PR from b*bapt2014-09-011-3/+0
* Remove expired ports:rene2014-04-181-2/+0
* Remove expired ports:rene2014-04-131-2/+0
* biology/seqtools: Tools for visualising sequence alignmentswg2013-11-101-1/+1
* - Disconnect ports removed in r325546bdrewery2013-08-291-1/+0
* KDE3 and QT3 expired on 2013-07-01, remove these ports.rene2013-07-271-1/+0
* Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.danfe2013-02-231-0/+1
* 2012-11-26 benchmarks/gsbench: No more public distfilesbapt2012-11-281-1/+0
* 2012-10-20 chinese/wangttf: No more public distfilesbapt2012-10-261-1/+0
* Add new ports biology/plink [1] and biology/plinkseq [2]:makc2012-09-271-0/+2
* SeqAn is an open source C++ library of efficient algorithmsamdmi32012-06-071-0/+1
* Bye bye abandonwares (part 2)bapt2011-08-011-5/+0
* Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.wen2011-04-221-0/+1
* p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XMLwen2010-03-011-0/+1
* python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)wen2009-12-291-0/+1
* pyfasta is a python module for fast, memory-efficient, pythonicwen2009-11-181-0/+1
* Velvet is a de novo genomic assembler specially designed for short readamdmi32009-11-071-0/+1
* Bio::SCF module allows you to read and update (in a restrictedmiwi2009-08-291-0/+1
* Io_lib is a library of file reading and writing code to provide amiwi2009-08-291-0/+1
* Bio::NEXUS package provides an object-oriented, Perl-basedmiwi2009-08-231-0/+1
* PhyML is a software that estimates maximum likelihood phylogenies fromamdmi32009-07-211-0/+1
* p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. Thismiwi2009-07-011-0/+1
* PyCogent is a software library for genomic biology. It is a fully integratedmiwi2009-06-221-0/+1
* Add the biology/crux port.jasone2009-06-091-0/+1
* 2009-05-31 biology/p5-bioperl-devel: no longer under developmentmiwi2009-06-061-2/+0
* LibSBML is an open-source programming library to help you read, write,miwi2009-05-291-0/+1
* Bio::Glite is an interface to G-language Genome Analysis Environmentmiwi2009-04-031-0/+1
* p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)miwi2009-03-111-0/+1
* - Delete biology/nab port after being marked DEPRECATED for three monthspav2008-07-241-1/+0
* SSAHA is a software tool for very fast matching and alignment of DNAlippe2008-06-211-0/+1
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-241-0/+1
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-241-0/+1
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-241-0/+1
* New port: biology/consed viewing and editing workbench for sequenceedwin2008-05-241-0/+1
* NJplot is a tree drawing program able to draw any phylogenetic tree expressedpav2008-05-141-0/+1
* MUSCLE is multiple alignment software for protein and nucleotide sequences.pav2008-05-141-0/+1
* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryrafan2008-04-061-0/+1
* MrBayes is a program for the Bayesian estimation of phylogeny.miwi2007-12-151-0/+1
* MUMmer is a modular system for the rapid whole genome alignment of finishedmiwi2007-12-151-0/+1
* - Sort category Makefilessat2007-10-061-2/+2
* Remove expired leaf port:vd2007-01-251-1/+0
* The BioCocoa framework provides developers with the opportunity to adddinoex2006-12-301-0/+1
* Adun is a new extendible molecular simulation program that alsodinoex2006-11-101-0/+1
* Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNAclsung2006-09-291-0/+1
* Folding@Home is a distributed computing project -- people from through out thepav2006-08-291-0/+1
* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedpav2006-06-201-0/+1
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.aaron2006-05-141-0/+1
* Add protomol 2.0.3, OO, component based, framework for molecularehaupt2006-05-061-0/+1
* Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-031-0/+1
* Bioperl-run contain modules that provides a PERL interface to variousgarga2006-05-031-0/+1
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofgarga2006-03-171-0/+1
* Add mafft 5.734, multiple sequence alignments based on fast Fouriergarga2006-03-151-0/+1
* Add dotter 20021204 # last modified date in FTP server, a viewer forgarga2006-03-151-0/+1
* Add blat 33, a fast tool for local sequence similarity searches.garga2006-03-151-0/+1
* Add belvu 2.29, a viewer for multiple sequence alignments.garga2006-03-151-0/+1
* Jalview is a multiple alignment editor written in Java. It is used widely in ahq2006-02-131-0/+1
* - Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoiddanfe2006-01-201-0/+1
* - Remove expired portspav2006-01-151-3/+0
* - Re-add p5-bioperl-devel, development version of biology/p5-bioperlbarner2005-12-031-0/+1
* Remove expired portskris2005-11-051-1/+0
* Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser forehaupt2005-10-161-0/+1
* Add p5-Bio-Das 1.02, client-side library for Distributed Genomegarga2005-09-011-0/+1
* - biology/act is redundant after biology/artemis updatesem2005-03-121-1/+0
* Add finchtv 1.3.0, a chromatogram trace viewer.thierry2005-03-121-0/+1
* As previously announced, remove ports that have reached their expiry date,kris2005-02-191-1/+0
* [new port] biology/embassysem2004-11-271-0/+1
* Add blast, a powerful software package for gene and protein identification,pav2004-11-121-0/+1
* Add ariadne 1.3, programs to compare protein sequences andkrion2004-06-221-0/+1
* Remove category pkg/COMMENT files in favour of a COMMENT variable in thekris2004-04-021-0/+2
* new port:biology/lsysexpedwin2003-09-031-0/+1
* As announced on May 6, remove the broken p5-bioperl-devel port.kris2003-08-081-1/+0
* A new port garlic, free molecular viewer and editor, free molecularmaho2003-07-281-0/+1
* Remove gaussian98kris2003-02-051-1/+0
* New Port: biology/actedwin2003-01-161-0/+1
* add treepuzzle 5.1ijliao2002-11-201-0/+1
* Connect distribfold to build after moving it from misc categorylioux2002-10-071-0/+1
* add primer3 0.9ijliao2002-09-171-0/+1
* Flip is used to find/translate orfs.dinoex2002-09-101-0/+1
* "Wise2 is package that is focused on comparing DNA sequences atdinoex2002-09-101-0/+1
* New port L-Breeder version 1.0: Allows you to display and breedlioux2002-08-211-0/+1
* Add pymol 0.82, Free and Open-Source molecular modeling system.perky2002-08-131-0/+1
* add libgenome 0.5.0ijliao2002-07-301-0/+1
* add avida 1.6.0ijliao2002-04-201-0/+1
* Swiss-PdbViewer is an application that provides a user friendly interfacedinoex2002-04-031-0/+1
* Add crimap 2.4, a tool for the creation of multilocus linkage maps.wjv2002-03-271-0/+1
* Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.wjv2002-03-271-0/+1
* Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.wjv2002-01-251-0/+1
* Initial import of artemis 4.0kevlo2001-12-221-0/+1
* Add gff2ps 0.97b, converts gff-formated genomic data-sets topetef2001-12-191-0/+1
* Add dna-qc 1993.07.26, a quality control algorithm for DNApetef2001-12-191-0/+1
* Add ruby-bio (BioRuby), an integrated environment for Bioinformaticsknu2001-10-241-0/+1
* Add nclever 4.0, a character-based version of NCBI's Entrez program.wjv2001-09-261-0/+1
* Add seqio 1.2.2, a set of C functions which can read/writewjv2001-08-221-0/+1
* Add treeviewx 0.1.1, a phylogenetic tree viewer.wjv2001-08-171-0/+1
* Add p5-bioperl-devel 0.9.0,wjv2001-08-141-0/+1
* Add lamarc 2001.08.06,wjv2001-08-071-0/+1
* Add recombine 1.40, a program to fit population models across sites.wjv2001-08-061-0/+1
* Add fluctuate 1.30, a program to fit population models.wjv2001-08-061-0/+1
* Add coalesce 1.50, a program to fit population models.wjv2001-08-061-0/+1
* Add migrate 1.2,wjv2001-08-061-0/+1
* Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogenywjv2001-07-041-0/+1
* reimport biology/genpakijliao2001-02-281-0/+1
* module name conflict with print/gp, so remove it and I'll reimport it againijliao2001-02-281-1/+0
* add gpijliao2001-02-281-0/+1
* - New port: biology/fasta3, which comprises the FASTA3 suite of DNA andjeh2001-02-121-0/+1
* New port: biology/fasta, the FASTA2 suite of DNA and protein sequencejeh2001-02-121-0/+1
* add gaussian98, an ab-initio molecular orbital calculation program.sf2001-02-111-0/+1
* New Port: biology/ncbi-toolkitjeh2000-10-291-0/+1
* Initial import of fastDNAml Version 1.2.2jeh2000-10-121-0/+1
* Initial import of biology/biojavajeh2000-10-101-0/+1
* This is nab (nucleic acid builder), a language for macromoleculesjeh2000-10-101-0/+1
* Add emboss, the European Molecular Biology Open Software Suitenbm2000-08-011-0/+1
* Add py-biopython, is a collection of Python packages and modules creatednbm2000-07-311-0/+1
* Add BioPerl, a collection of Perl5 mods for bioinformatics/genomicsnbm2000-07-281-0/+1
* Add p5-AcePerl, a perl interface to the ACEDB genome database systemnbm2000-07-281-0/+1
* Add sim4, an implementation of the sim4 algorithm for aligning expressednbm2000-07-271-0/+1
* Add xdrawchem 0.82 - a program for drawing moleculesalex2000-07-191-0/+1
* Activating the chemeq, clustalw, paml, and phylip ports.steve2000-07-101-0/+4
* Added gperiodic and xmolwttaoka1999-09-071-0/+2
* Change Id->FreeBSD.obrien1999-08-251-1/+1
* Added deft and ortep3taoka1999-05-191-1/+3
* Add platon and moldentaoka1999-05-071-1/+3
* Add mopac and psi88 (Move mopac and psi88 from misc to biology)taoka1999-05-061-1/+3
* Activate tinker.jkoshy1998-11-171-1/+2
* Turn on hmmer.steve1998-07-131-1/+2
* Activate povchem.vanilla1998-03-161-1/+2
* Activate kinemagejseger1998-01-301-1/+2
* Activate seaview.vanilla1997-12-221-1/+2
* Activate babel.vanilla1997-12-221-1/+2
* Activate rasmol.vanilla1997-12-161-2/+2
* The new ports category "biology" starts here today. No Darwinasami1997-12-131-0/+6
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