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FreeBSD GNOME current development ports (https://github.com/freebsd/freebsd-ports-gnome)
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* biology/py-biom-format: Restore in preparation for an update to v2.1.8Joseph Mingrone2020-09-251-0/+1
* Remove expired ports:Rene Ladan2020-09-191-2/+0
* Remove expired ports:Rene Ladan2020-08-271-1/+0
* Remove deprecated ports:Rene Ladan2020-08-151-1/+0
* Add rubygem-bio-shell 1.0.0Sunpoet Po-Chuan Hsieh2020-07-241-0/+1
* Add rubygem-bio-old-biofetch-emulator 1.0.0Sunpoet Po-Chuan Hsieh2020-07-241-0/+1
* Add rubygem-bio-executables 1.0.0Sunpoet Po-Chuan Hsieh2020-07-241-0/+1
* biology/picard-tools: CLI tools for manipulating sequencing dataJason W. Bacon2020-06-131-0/+1
* biology/bioawk: BWK awk modified for biological dataJason W. Bacon2020-06-051-0/+1
* biology/subread: Read alignment, quantification and mutation discoveryJason W. Bacon2020-06-051-0/+1
* bioloty/vt: Discovers short variants from Next Generation Sequencing dataJason W. Bacon2020-06-051-0/+1
* New port: biology/py-hits: Utilities for processing high-throughput sequencin...Yuri Victorovich2020-05-161-0/+1
* New port: biology/py-scikit-bio: Data structures, algorithms, educational res...Yuri Victorovich2020-05-161-0/+1
* New port: biology/py-pandas-charm: Library for getting character matrices int...Yuri Victorovich2020-05-161-0/+1
* New port: biology/py-ete3: Framework for the analysis and visualization of treesYuri Victorovich2020-05-161-0/+1
* New port: biology/scrm: Coalescent simulator for biological sequencesYuri Victorovich2020-05-151-0/+1
* - Resurrect and unbreak by updating to version 34.0Alexey Dokuchaev2020-05-101-0/+1
* Remove expired ports:Rene Ladan2020-05-051-5/+0
* biology/plink: Whole genome association analysis toolsetJason W. Bacon2020-05-051-0/+1
* biology/gcta: Genome-wide Complex Trait AnalysisJason W. Bacon2020-04-151-0/+1
* Resurrect biology/linux-foldingathomeMateusz Piotrowski2020-03-221-0/+1
* Remove expired ports:Rene Ladan2020-01-271-2/+0
* Add p5-Bio-Variation 1.7.4Sunpoet Po-Chuan Hsieh2019-12-091-0/+1
* Add p5-Bio-DB-NCBIHelper 1.7.6Sunpoet Po-Chuan Hsieh2019-12-091-0/+1
* Add p5-Bio-DB-EMBL 1.7.4Sunpoet Po-Chuan Hsieh2019-12-091-0/+1
* Remove expired ports:Rene Ladan2019-10-161-2/+0
* biology/tophat: Fast splice junction mapper for RNA-Seq readsJason W. Bacon2019-09-271-0/+1
* biology/py-multiqc: Aggregate bioinformatics analysis reportsJason W. Bacon2019-09-241-0/+1
* biology/haplohseq: Identify regions of allelic imbalanceJason W. Bacon2019-09-161-0/+1
* New port: biology/libbigwig: C library for handling bigWig files (containing ...Yuri Victorovich2019-07-121-0/+1
* New port: biology/viennarna: Alignment tools for the structural analysis of RNAYuri Victorovich2019-06-241-0/+1
* New port: biology/treekin: Efficient computation of RNA folding dynamicsYuri Victorovich2019-06-161-0/+1
* biology/bolt-lmm: Mixed model association testing and variance component anal...Jason W. Bacon2019-05-261-0/+1
* New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their...Yuri Victorovich2019-05-261-0/+1
* New port: biology/mothur: Software for bioinformatics of the microbial ecolog...Yuri Victorovich2019-05-211-0/+1
* New port: biology/hhsuite: Remote protein homology detection suiteYuri Victorovich2019-05-191-0/+1
* biology/gemma: Genome-wide Efficient Mixed Model AssociationJason W. Bacon2019-05-171-0/+1
* biology/vsearch: Versatile open-source tool for metagenomicsJason W. Bacon2019-05-101-0/+1
* biology/fastp: Ultra-fast all-in-one FASTQ preprocessorJason W. Bacon2019-05-031-0/+1
* biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequencesJason W. Bacon2019-04-251-0/+1
* biology/star: Spliced Transcripts Alignment to a ReferenceJason W. Bacon2019-04-221-0/+1
* New port: biology/py-xenaPython: API for Xena Hub to access genetic informati...Yuri Victorovich2019-04-131-0/+1
* biology/py-dnaio: Read and write FASTQ and FASTAJason W. Bacon2019-03-251-0/+1
* Qt4 deprecation: Remove Qt4 and its consumes.Tobias C. Berner2019-03-171-1/+0
* New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end se...Yuri Victorovich2019-02-251-0/+1
* Add p5-Bio-Cluster 1.7.3Sunpoet Po-Chuan Hsieh2019-02-211-0/+1
* New port: biology/figtree: Graphical viewer of phylogenetic treesYuri Victorovich2019-02-041-0/+1
* New port: biology/graphlan: High-quality circular representations of taxonomi...Yuri Victorovich2019-02-041-0/+1
* New port: biology/prodigy-lig: Prediction of protein-small molecule binding a...Yuri Victorovich2019-02-041-0/+1
* New port: biology/prodigal: Protein-coding gene prediction for prokaryotic ge...Yuri Victorovich2019-02-041-0/+1
* New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein descripti...Yuri Victorovich2019-01-291-0/+1
* Sort categories Makefiles.Mathieu Arnold2019-01-231-1/+1
* New port: biology/hisat2: Program for mapping next-generation sequencing readsJason W. Bacon2019-01-121-0/+1
* Remove expired ports:Rene Ladan2018-12-211-1/+0
* New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNEYuri Victorovich2018-12-151-0/+1
* Remove biology/njplotJoseph Mingrone2018-12-111-1/+0
* New port: math/checkm: Quality assessment tool for the microbial genomesYuri Victorovich2018-12-071-0/+1
* New port: math/groopm: Metagenomic binning suiteYuri Victorovich2018-12-071-0/+1
* New port: biology/gatk: Variant discovery in high-throughput sequencing dataYuri Victorovich2018-12-031-0/+1
* New port: biology/py-gffutils: Work with GFF and GTF files in a flexible data...Yuri Victorovich2018-10-191-0/+1
* New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subse...Yuri Victorovich2018-10-191-0/+1
* New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) f...Yuri Victorovich2018-10-191-0/+1
* New port: biology/ncbi-cxx-toolkit: NCBI C++ ToolkitYuri Victorovich2018-10-081-0/+1
* biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/Yuri Victorovich2018-10-071-1/+0
* New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq dataYuri Victorovich2018-09-211-0/+1
* Remove expired ports:Rene Ladan2018-08-171-1/+0
* Regular sorting of categories Makefiles.Mathieu Arnold2018-08-081-1/+1
* New port: biology/py-orange3-single-cell: Orange add-on for gene expression o...Yuri Victorovich2018-08-071-0/+1
* New port: biology/exonerate: Generic tool for sequence alignmentYuri Victorovich2018-07-131-0/+1
* New port: biology/stringtie: Transcript assembly and quantification for RNA-seqYuri Victorovich2018-07-121-0/+1
* New port: biology/cytoscape: Software to visualize molecular interaction netw...Yuri Victorovich2018-07-031-0/+1
* New port: biology/igv: Visualization tool for genomic datasetsYuri Victorovich2018-06-261-0/+1
* New port: biology/py-orange3-bioinformatics: Orange add-on providing common f...Yuri Victorovich2018-06-141-0/+1
* New port: biology/py-Genesis-PyAPI: API for the Genesis platform for genetics...Yuri Victorovich2018-06-131-0/+1
* New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Se...Yuri Victorovich2018-06-111-0/+1
* Remove expired ports:Rene Ladan2018-06-071-4/+0
* Add new port: biology/infernalKirill Ponomarev2018-06-061-0/+1
* biology/clustal-omega: Multiple alignment of nucleic acid and protein, replac...Jason W. Bacon2018-05-221-0/+1
* biology/clustalx: Multiple alignment of nucleic acid and protein sequences wi...Jason W. Bacon2018-05-221-0/+1
* New port, biology/hyphy: Hypothesis testing using PhylogeniesJoseph Mingrone2018-05-111-0/+1
* biology/unanimity: Pacific Biosciences consensus library and applicationsJason W. Bacon2018-04-241-0/+1
* biology/pbcopper: Core C++ library for Pacific Biosciences toolsJason W. Bacon2018-04-241-0/+1
* biology/pbbam: PacBio BAM C++ library, with SWIG bindingsJason W. Bacon2018-04-241-0/+1
* biology/pbseqan: Pacific Biosciences patched and stripped down SeqAnJason W. Bacon2018-04-221-0/+1
* biology/ddocent: Bash pipeline for RAD sequencingJason W. Bacon2018-04-201-0/+1
* biology/freebayes: Bayesian haplotype-based polymorphism discovery and genoty...Jason W. Bacon2018-04-201-0/+1
* biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF filesJason W. Bacon2018-04-171-0/+1
* biology/fastahack: Utility for indexing and sequence extraction from FASTA filesJason W. Bacon2018-04-161-0/+1
* biology/smithwaterman: Smith-waterman-gotoh alignment algorithmJason W. Bacon2018-04-161-0/+1
* biology/tabixpp: C++ wrapper to tabix indexerJason W. Bacon2018-04-151-0/+1
* biology/pear-merger: Memory-efficient and accurate paired-end read mergerJason W. Bacon2018-04-051-0/+1
* biology/seqtk: Tool for processing sequences in FASTA/FASTQ formatJason W. Bacon2018-04-041-0/+1
* biology/trimadap: Trim adapter sequences from Illumina dataJason W. Bacon2018-04-041-0/+1
* biology/rainbow: Efficient clustering and assembling of short readsJason W. Bacon2018-04-031-0/+1
* biology/stacks: Software pipeline for building loci from short-read sequencesJason W. Bacon2018-03-311-0/+1
* biology/bamtools: API and toolkit for handling BAM filesJason W. Bacon2018-03-281-0/+1
* [new port] biology/canu: Single molecule sequence assemblerJason W. Bacon2017-12-221-0/+1
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adap...Jason W. Bacon2017-12-091-0/+1
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)...Jason W. Bacon2017-12-031-0/+1
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ...Jason W. Bacon2017-12-031-0/+1
* [new port] biology/fastqc: Quality control tool for high throughput sequence ...Jason W. Bacon2017-12-011-0/+1
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, poJason W. Bacon2017-11-301-0/+1
* New port, biology/iqtree: Efficient phylogenomic softwareJoseph Mingrone2017-10-221-0/+1
* Add p5-Bio-FeatureIO 1.6.905Sunpoet Po-Chuan Hsieh2017-09-161-0/+1
* Remove expired ports:Rene Ladan2017-08-231-1/+0
* bx-python is a python library and associated set of scripts to allow for rapidMartin Wilke2017-05-061-0/+1
* pysam is a lightweight wrapper of the htslib C-API and provides facilities toMartin Wilke2017-05-061-0/+1
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (goog...Larry Rosenman2017-04-301-1/+0
* Move devel/rubygem-bio to biology/rubygem-bioSunpoet Po-Chuan Hsieh2017-02-051-0/+1
* - Add p5-Bio-Coordinate 1.007001Sunpoet Po-Chuan Hsieh2016-12-191-0/+1
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-RunSunpoet Po-Chuan Hsieh2016-12-181-1/+1
* - Move biology/p5-bioperl to biology/p5-BioPerlSunpoet Po-Chuan Hsieh2016-12-181-1/+1
* biology/njplot: Revive and update to version 2.4Joseph Mingrone2016-11-161-0/+1
* Remove expired ports without open PRs:Rene Ladan2016-07-051-1/+0
* biology/seqan: update 1.3.1 -> 2.1.1Jason Unovitch2016-05-101-0/+1
* New port: biology/seqan-appsJason Unovitch2016-05-101-0/+1
* The BIOM file format (canonically pronounced biome) is designed to be aOlivier Duchateau2016-05-101-0/+1
* DNA query sequences against a protein reference database (BLASTP and BLASTXWen Heping2016-05-061-0/+1
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.Dmitry Marakasov2016-03-241-0/+1
* New port: biology/bowtie2.Raphael Kubo da Costa2016-03-231-0/+1
* New port: biology/slclust.Raphael Kubo da Costa2016-03-231-0/+1
* Trimmomatic performs a variety of useful trimming tasks for illuminaWen Heping2016-03-171-0/+1
* New port: biology/p5-transdecoderKurt Jaeger2016-03-171-0/+1
* New port: biology/bowtie.Raphael Kubo da Costa2016-03-051-0/+1
* New port: biology/vcftools.Raphael Kubo da Costa2016-02-271-0/+1
* The bedtools utilities are a suite of tools for performing a wide range ofWen Heping2016-01-191-0/+1
* Remove expired ports:Rene Ladan2015-11-291-3/+0
* BWA is a program for aligning sequencing reads against a large referenceRuslan Makhmatkhanov2015-09-261-0/+1
* Fast indexing and retrieval of FASTA records from flat file data bases.Ruslan Makhmatkhanov2015-09-261-0/+1
* Simple and quick FastQ and FastA tool for file reading and conversion.Ruslan Makhmatkhanov2015-09-261-0/+1
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromRuslan Makhmatkhanov2015-09-261-0/+1
* The FASTX-Toolkit is a collection of command line tools for Short-ReadsRuslan Makhmatkhanov2015-09-261-0/+1
* Gordon's text utilities.Ruslan Makhmatkhanov2015-09-261-0/+1
* CD-HIT is a very widely used program for clustering and comparing protein orWen Heping2015-09-191-0/+1
* New port: biology/bcftoolsKurt Jaeger2015-06-061-0/+1
* Remove expired ports:Rene Ladan2015-01-011-1/+0
* Rename biology/ncbi-blast to biology/ncbi-blast+Michael Gmelin2014-12-311-1/+1
* Samtools implements various utilities for post-processing alignments in thePawel Pekala2014-12-161-0/+1
* HTSlib is an implementation of a unified C library for accessing common filePawel Pekala2014-12-151-0/+1
* Add new port biology/ncbi-blastJohn Marino2014-10-071-0/+1
* Second run at cleaning out non staged ports without pending PRBaptiste Daroussin2014-09-021-1/+0
* Remove non staged ports without pending PR from b*Baptiste Daroussin2014-09-011-3/+0
* Remove expired ports:Rene Ladan2014-04-181-2/+0
* Remove expired ports:Rene Ladan2014-04-131-2/+0
* biology/seqtools: Tools for visualising sequence alignmentsWilliam Grzybowski2013-11-101-1/+1
* - Disconnect ports removed in r325546Bryan Drewery2013-08-291-1/+0
* KDE3 and QT3 expired on 2013-07-01, remove these ports.Rene Ladan2013-07-271-1/+0
* Add Unipro UGENE, a free open-source crowss-platform bioinformatics software.Alexey Dokuchaev2013-02-231-0/+1
* 2012-11-26 benchmarks/gsbench: No more public distfilesBaptiste Daroussin2012-11-281-1/+0
* 2012-10-20 chinese/wangttf: No more public distfilesBaptiste Daroussin2012-10-261-1/+0
* Add new ports biology/plink [1] and biology/plinkseq [2]:Max Brazhnikov2012-09-271-0/+2
* SeqAn is an open source C++ library of efficient algorithmsDmitry Marakasov2012-06-071-0/+1
* Bye bye abandonwares (part 2)Baptiste Daroussin2011-08-011-5/+0
* Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.Wen Heping2011-04-221-0/+1
* p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XMLWen Heping2010-03-011-0/+1
* python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)Wen Heping2009-12-291-0/+1
* pyfasta is a python module for fast, memory-efficient, pythonicWen Heping2009-11-181-0/+1
* Velvet is a de novo genomic assembler specially designed for short readDmitry Marakasov2009-11-071-0/+1
* Bio::SCF module allows you to read and update (in a restrictedMartin Wilke2009-08-291-0/+1
* Io_lib is a library of file reading and writing code to provide aMartin Wilke2009-08-291-0/+1
* Bio::NEXUS package provides an object-oriented, Perl-basedMartin Wilke2009-08-231-0/+1
* PhyML is a software that estimates maximum likelihood phylogenies fromDmitry Marakasov2009-07-211-0/+1
* p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. ThisMartin Wilke2009-07-011-0/+1
* PyCogent is a software library for genomic biology. It is a fully integratedMartin Wilke2009-06-221-0/+1
* Add the biology/crux port.Jason Evans2009-06-091-0/+1
* 2009-05-31 biology/p5-bioperl-devel: no longer under developmentMartin Wilke2009-06-061-2/+0
* LibSBML is an open-source programming library to help you read, write,Martin Wilke2009-05-291-0/+1
* Bio::Glite is an interface to G-language Genome Analysis EnvironmentMartin Wilke2009-04-031-0/+1
* p5-Bio-Graphics is a simple GD-based renderer (diagram drawer)Martin Wilke2009-03-111-0/+1
* - Delete biology/nab port after being marked DEPRECATED for three monthsPav Lucistnik2008-07-241-1/+0
* SSAHA is a software tool for very fast matching and alignment of DNAFelippe de Meirelles Motta2008-06-211-0/+1
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-241-0/+1
* NJplot is a tree drawing program able to draw any phylogenetic tree expressedPav Lucistnik2008-05-141-0/+1
* MUSCLE is multiple alignment software for protein and nucleotide sequences.Pav Lucistnik2008-05-141-0/+1
* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryRong-En Fan2008-04-061-0/+1
* MrBayes is a program for the Bayesian estimation of phylogeny.Martin Wilke2007-12-151-0/+1
* MUMmer is a modular system for the rapid whole genome alignment of finishedMartin Wilke2007-12-151-0/+1
* - Sort category MakefilesAndrew Pantyukhin2007-10-061-2/+2
* Remove expired leaf port:Vasil Dimov2007-01-251-1/+0
* The BioCocoa framework provides developers with the opportunity to addDirk Meyer2006-12-301-0/+1
* Adun is a new extendible molecular simulation program that alsoDirk Meyer2006-11-101-0/+1
* Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNACheng-Lung Sung2006-09-291-0/+1
* Folding@Home is a distributed computing project -- people from through out thePav Lucistnik2006-08-291-0/+1
* SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculatedPav Lucistnik2006-06-201-0/+1
* Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.Aaron Dalton2006-05-141-0/+1
* Add protomol 2.0.3, OO, component based, framework for molecularEmanuel Haupt2006-05-061-0/+1
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-031-0/+1
* Bioperl-run contain modules that provides a PERL interface to variousRenato Botelho2006-05-031-0/+1
* Add lagan 1.2, efficient tools for large-scale multiple alignments ofRenato Botelho2006-03-171-0/+1
* Add mafft 5.734, multiple sequence alignments based on fast FourierRenato Botelho2006-03-151-0/+1
* Add dotter 20021204 # last modified date in FTP server, a viewer forRenato Botelho2006-03-151-0/+1
* Add blat 33, a fast tool for local sequence similarity searches.Renato Botelho2006-03-151-0/+1
* Add belvu 2.29, a viewer for multiple sequence alignments.Renato Botelho2006-03-15