Gentoo Packages

Category: sci-biology

• sci-biology/ABI-connectivity-data::science - Ebuilds: 2, Testing: 0.2
  Description: Connectivity data from the Allen Mouse Brain data portal
  Homepage: https://github.com/IBT-FMI/ABI-connectivity-data_generator
  License: fairuse
• sci-biology/ABI-expression-data::science - Ebuilds: 1, Testing: 0.2
  Description: Gene expression data form the Allen Mouse Brain data portal
  Homepage: https://github.com/IBT-FMI/ABI-expression-data_generator
  License: fairuse
• sci-biology/ANGLE-bin::science - Ebuilds: 1, Testing: 20080813-r1
  Description: CDS prediction overcoming sequencing errors in unfinished cDNA
  Homepage: http://bioinformatics.cenargen.embrapa.br/portrait/download
  License: BSD
• sci-biology/AlignGraph::science - Ebuilds: 1, Snapshot: 9999
  Description: Reference-genome-assisted asssembly of contigs/scaffolds using PE reads
  Homepage: https://github.com/baoe/AlignGraph http://bioinformatics.oxfordjournals.org/content/30/12/i319.long
  License: Artistic-2
• sci-biology/BEP032tools::science - Ebuilds: 1, Testing: 0.0.1_alpha
  Description: Conversion and validation tools for BEP 032
  Homepage: https://github.com/INT-NIT/BEP032tools
  License: MIT
• sci-biology/BRAKER::science - Ebuilds: 1, Testing: 2.1.2
  Description: Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS
  Homepage: https://github.com/Gaius-Augustus/BRAKER http://bioinf.uni-greifswald.de/bioinf/braker http://bioinf.uni-greifswald.de/augustus/downloads
  License: Artistic
• sci-biology/BRANCH::science - Ebuilds: 1, Snapshot: 9999
  Description: Extend partial transcripts with sequence from other reads or genomic contigs
  Homepage: https://github.com/baoe/BRANCH
  License: Artistic-2
• sci-biology/CAT::science - Ebuilds: 1, Testing: 1.3
  Description: Codon usage bias (composition) and its statistical significance
  Homepage: https://bigd.big.ac.cn/tools/cat
  License: GPL-3+
• sci-biology/FLASH::science - Ebuilds: 1, Testing: 1.2.11
  Description: Paired-end mates merge from fragments
  Homepage: https://sourceforge.net/projects/flashpage/
  License: GPL-3
• sci-biology/Fastaq::science - Ebuilds: 1, Testing: 3.18.0
  Description: Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers
  Homepage: https://github.com/sanger-pathogens/Fastaq
  License: GPL-3
• sci-biology/GAL::science - Ebuilds: 1, Testing: 0.2.2_p20200508
  Description: Genome Annotation Library (incl. fasta_tool)
  Homepage: https://github.com/The-Sequence-Ontology/GAL
  License: ( GPL-1+ Artistic )
• sci-biology/IMAGE::science - Ebuilds: 1, Testing: 2.4.1
  Description: Iterative Mapping and Assembly for Gap Elimination using paired-end Illumina
  Homepage: https://sourceforge.net/apps/mediawiki/image2
  License: CC-BY-2.0
• sci-biology/KING::science - Ebuilds: 1, Testing: 2.2.7
  Description: Check family relationship and infer population structure
  Homepage: https://kingrelatedness.com
  License: all-rights-reserved
• sci-biology/KaKs_Calculator::science - Ebuilds: 2, Testing: 2.0
  Description: Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates
  Homepage: https://sourceforge.net/projects/kakscalculator2/ https://www.sciencedirect.com/science/article/pii/S1672022910600083
  License: GPL-3
• sci-biology/LINKS::science - Ebuilds: 1, Testing: 2.0.1
  Description: Scaffold genome assemblies by Chromium/PacBio/Nanopore reads
  Homepage: https://github.com/bcgsc/LINKS
  License: GPL-3
• sci-biology/MaSuRCA::science - Ebuilds: 2
  Description: de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore
  Homepage: http://www.genome.umd.edu/masurca.html http://bioinformatics.oxfordjournals.org/content/29/21/2669 https://github.com/alekseyzimin/masurca
  License: BSD GPL-2 GPL-3
• sci-biology/MeV::science - Ebuilds: 1, Testing: 4.8.1
  Description: Multiple experiment Viewer for genomic data analysis
  Homepage: https://sourceforge.net/projects/mev-tm4/
  License: Artistic-2
• sci-biology/MochiView::science - Ebuilds: 1, Testing: 1.46-r1
  Description: Genome browser and analysis
  Homepage: https://www.johnsonlab.ucsf.edu/mochi.html
  License: MIT LGPL-3 MPL-1.1 Apache-2.0
• sci-biology/MuSeqBox::science - Ebuilds: 1, Testing: 5.7.2021
  Description: Parse and filter BLAST output into tab-delimited file
  Homepage: http://brendelgroup.org/bioinformatics2go/MuSeqBox.php
  License: GPL-3
• sci-biology/NGSEPcore::science - Ebuilds: 1, Testing: 4.0.3
  Description: NGSEP (CNV and indel discovery)
  Homepage: https://sourceforge.net/p/ngsep/wiki/Home https://github.com/NGSEP/NGSEPcore
  License: GPL-3
• sci-biology/NGSEPcore-bin::science - Ebuilds: 1, Testing: 4.0.3
  Description: NGSEP (CNV and indel discovery)
  Homepage: https://sourceforge.net/p/ngsep/wiki/Home https://github.com/NGSEP/NGSEPcore
  License: GPL-3
• sci-biology/ONTO-PERL::science - Ebuilds: 1, Testing: 1.45
  Description: Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology)
  Homepage: https://metacpan.org/release/ONTO-PERL
• sci-biology/ParaAT::science - Ebuilds: 1, Testing: 1.0
  Description: Create multiple protein-coding DNA alignments and back-Translation
  Homepage: http://cbb.big.ac.cn/software https://www.sciencedirect.com/science/article/pii/S0006291X12003518
  License: GPL-3
• sci-biology/RAILS::science - Ebuilds: 1, Testing: 1.5.1
  Description: Cobbler and RAILS scaffolding tools acting on SAM streams
  Homepage: https://github.com/bcgsc/RAILS
  License: GPL-3+
• sci-biology/Rcorrector::science - Ebuilds: 1, Testing: 1.0.4
  Description: Error correction for Illumina RNA-seq reads
  Homepage: https://github.com/mourisl/Rcorrector
  License: GPL-2+
• sci-biology/SEECER::science - Ebuilds: 2, Testing: 0.1.3-r3
  Description: SEquence Error Corrector for RNA-Seq reads
  Homepage: http://sb.cs.cmu.edu/seecer/
  License: GPL-3
• sci-biology/SPAdes::science - Ebuilds: 1, Testing: 3.15.5
  Description: truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. dipspades is assembly module for highly polymorphic diploid genomes
  Homepage: https://cab.spbu.ru/software/spades
  License: GPL-2
• sci-biology/SSAKE::science - Ebuilds: 1, Testing: 3.8.2
  Description: Short-read trimmer, OLC assembler, scaffolder in PERL using the 3'-most k-mers
  Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ssake
  License: GPL-2+
• sci-biology/SnpEff::science - Ebuilds: 1, Testing: 4.3t
  Description: SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF
  Homepage: https://pcingola.github.io/SnpEff/
  License: LGPL-3
• sci-biology/SolexaQA::science - Ebuilds: 1, Testing: 3.1.7.1
  Description: Analyze and trim single-end and paired-end reads, show quality statistics
  Homepage: https://sourceforge.net/projects/solexaqa
  License: GPL-3
• sci-biology/TransDecoder::science - Ebuilds: 1, Testing: 5.5.0
  Description: Extract ORF/CDS regions from FASTA sequences
  Homepage: https://github.com/TransDecoder/TransDecoder/wiki
  License: BSD-BroadInstitute
• sci-biology/VarScan::science - Ebuilds: 1, Testing: 2.4.4
  Description: Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)
  Homepage: http://varscan.sourceforge.net/
  License: Non-profit-OSL-3.0
• sci-biology/VarScan-bin::science - Ebuilds: 1, Testing: 2.4.4
  Description: Variant detection (germline, multi-sample, somatic mut., CNA), SNP
  Homepage: http://dkoboldt.github.io/varscan
  License: Non-profit-OSL-3.0
• sci-biology/VelvetOptimiser::science - Ebuilds: 1, Testing: 2.2.6
  Description: Optimise Velvet sequence assembler
  Homepage: https://vicbioinformatics.com/software.velvetoptimiser.shtml
  License: GPL-2
• sci-biology/YASRA::science - Ebuilds: 1, Testing: 2.33
  Description: Yet Another Short Read Assembler aligning to a reference using LASTZ
  Homepage: http://www.bx.psu.edu/miller_lab/
  License: GPL-2
• sci-biology/abacas::science - Ebuilds: 1, Testing: 1.3.1
  Description: Order and orientate DNA contigs even via 6-frame protein alignments
  Homepage: https://abacas.sourceforge.net
  License: GPL-2+
• sci-biology/act-bin::science - Ebuilds: 1, Testing: 17.0.1
  Description: DNA contig sequence comparison tool supplementing Artemis
  Homepage: https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
  License: GPL-2
• sci-biology/afni::science - Ebuilds: 3, Testing: 24.1.16
  Description: Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity.
  Homepage: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/
  License: GPL-3+
• sci-biology/afni-datasets::science - Ebuilds: 1, Testing: 20240503
  Description: Datasets for using and testing sci-biology/afni
  Homepage: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/
  License: GPL-3+
• sci-biology/aghermann::science - Ebuilds: 1, Testing: 1.1.2-r2
  Description: Aghermann is a program designed around a common workflow in sleep-research, complete with scoring facility; cairo subpixel drawing on screen or to file; conventional PSD and EEG Micrcontinuity profiles; Independent Component Analysis; artifact detection; and Process S simulation following Achermann et al, 1993.
  Homepage: http://johnhommer.com/academic/code/aghermann
  License: GPL-2+
• sci-biology/align_to_scf::science - Ebuilds: 1, Testing: 1.06
  Description: View trace information at a given position missing from Roche .ace files
  Homepage: http://genome.imb-jena.de/software/roche454ace2caf
  License: FLI-Jena
• sci-biology/angsd::science - Ebuilds: 1, Testing: 0.933
  Description: Population genetics analysis package
  Homepage: http://www.popgen.dk/angsd
  License: GPL-2
• sci-biology/assembly-stats::science - Ebuilds: 1, Snapshot: 9999
  Description: Assembly statistics (min, max, sum, N50, N90, count gaps and Ns)
  Homepage: https://github.com/martinghunt/assembly-stats
  License: GPL-3
• sci-biology/bam-readcount::science - Ebuilds: 2, Testing: 0.8.0, Snapshot: 9999
  Description: Count DNA sequence reads in BAM files and other statistics calculations
  Homepage: https://github.com/genome/bam-readcount
  License: MIT
• sci-biology/bambus::science - Ebuilds: 1, Testing: 2.33-r2
  Description: Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.
  Homepage: https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS https://sourceforge.net/projects/amos/files/bambus
  License: Artistic
• sci-biology/bamql::science - Ebuilds: 2, Testing: 1.6.1, Snapshot: 9999
  Description: Extract reads from BAM files
  Homepage: https://github.com/BoutrosLaboratory/bamql https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y
  License: MIT
• sci-biology/barrnap::science - Ebuilds: 1, Testing: 0.9
  Description: Predict Bacterial and Archaeal rRNA genes and output in GFF3 format
  Homepage: https://github.com/tseemann/barrnap
  License: GPL-3
• sci-biology/beagle::science - Ebuilds: 1, Testing: 5.1
  Description: Genotype calling/phasing, imputation of ungenotyped markers
  Homepage: https://faculty.washington.edu/browning/beagle/beagle.html
  License: GPL-3+
• sci-biology/bedops::science - Ebuilds: 2, Testing: 2.4.39
  Description: Manipulate BED file (alternative to bedtools)
  Homepage: http://bedops.readthedocs.io https://github.com/bedops/bedops
  License: GPL-2
• sci-biology/bidsschematools::science - Ebuilds: 1, Testing: 0.7.1
  Description: A Python library for working with the BIDS schema
  Homepage: https://github.com/bids-standard/bids-specification
  License: MIT
• sci-biology/biobambam2::science - Ebuilds: 2, Testing: 2.0.146, Snapshot: 9999
  Description: This package contains some tools for processing BAM files including bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
  Homepage: https://gitlab.com/german.tischler/biobambam2 https://github.com/gt1/biobambam2
  License: GPL-3 MIT
• sci-biology/bismark::science - Ebuilds: 1, Testing: 0.23.0
  Description: Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are: (1) Bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignments; (3) Supports ungapped and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context.
  Homepage: https://www.bioinformatics.babraham.ac.uk/projects/
  License: GPL-3+
• sci-biology/brat::science - Ebuilds: 1, Testing: 1.2.4
  Description: Bisulfite-treated Reads Analysis Tool (short read mapper)
  Homepage: http://compbio.cs.ucr.edu/brat/
  License: GPL-3
• sci-biology/brat_bw::science - Ebuilds: 1, Testing: 2.0.1
  Description: Bisulfite-aware short read mapper, FM-index, no InDel support
  Homepage: http://compbio.cs.ucr.edu/brat/
  License: GPL-3
• sci-biology/brat_nova::science - Ebuilds: 1, Testing: 20160103
  Description: Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align
  Homepage: http://compbio.cs.ucr.edu/brat/
  License: GPL-3
• sci-biology/brkraw::science - Ebuilds: 1, Testing: 0.3.11
  Description: Fast and easy statistical learning on NeuroImaging data
  Homepage: https://github.com/BrkRaw/brkraw
  License: GPL-3
• sci-biology/bru2nii::science - Ebuilds: 1, Testing: 1.0.20180303
  Description: This is a simple tool for converting Bruker ParaVision MRI data to the NIfTI file format. It includes both a drag-and-drop graphical interface (Bru2Nii) as well as a command line tool (Bru2).
  Homepage: https://github.com/neurolabusc/Bru2Nii
  License: || ( Artistic GPL-1+ )
• sci-biology/btl_bloomfilter::science - Ebuilds: 1, Testing: 1.2.1
  Description: BTL C/C common bloom filters
  Homepage: https://github.com/bcgsc/btl_bloomfilter
  License: GPL-3
• sci-biology/bx-python::science - Ebuilds: 1, Testing: 0.14.0
  Description: Library for rapid implementation of genome scale analyses
  Homepage: https://github.com/bxlab/bx-python
  License: MIT
• sci-biology/cast-bin::science - Ebuilds: 1, Testing: 20080813
  Description: Predict low-complexity regions in putative proteins
  Homepage: http://bioinformatics.cenargen.embrapa.br/portrait/download
  License: GPL-2
• sci-biology/cdbfasta::science - Ebuilds: 1, Testing: 0.1
  Description: FASTA record indexing/retrievieng utility
  Homepage: https://github.com/gpertea/cdbfasta
  License: Artistic
• sci-biology/cluster::science - Ebuilds: 1, Testing: 1.59
  Description: Hierarchical, k-means, k-medians clustering for expression/microarray analysis
  Homepage: http://bonsai.hgc.jp/~mdehoon/software/cluster http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv
  License: Eisen
• sci-biology/cnrun::science - Ebuilds: 1, Testing: 2.1.0-r2
  Description: CNrun is a neuronal network simulator, with these features: * a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and Alpha-Beta synapses; * a 6-5 Runge-Kutta integration method: slow but precise, adjustable; * Poisson, Van der Pol, Colpitts oscillators and interface for external stimulation sources; * NeuroML network topology import/export; * logging state variables, spikes; * implemented as a Lua module, for scripting model behaviour (e.g., to enable plastic processes regulated by model state); * interaction (topology push/pull, async connections) with other cnrun models running elsewhere on a network, with interactions (planned). Note that there is no `cnrun' executable, which existed in cnrun-1.*. Instead, you write a script for your simulation in Lua, and execute it as detailed in /usr/share/lua-cnrun/examples/example1.lua.
  Homepage: http://johnhommer.com/academic/code/cnrun
  License: GPL-2+
• sci-biology/codonw::science - Ebuilds: 1, Testing: 1.4.4-r2
  Description: Multivariate statistical analysis of codon and amino acid usage
  Homepage: https://codonw.sourceforge.net/
  License: GPL-2
• sci-biology/conform-gt::science - Ebuilds: 1, Testing: 1174
  Description: Modify your Variant Call Format file to be consistent with reference VCF
  Homepage: https://faculty.washington.edu/browning/conform-gt.html
  License: Apache-2.0 MIT
• sci-biology/coral::science - Ebuilds: 1, Testing: 1.4.1
  Description: Error corrector for Illumina and Roche/454 reads using multiple alignment info
  Homepage: https://www.cs.helsinki.fi/u/lmsalmel/coral
  License: GPL-3
• sci-biology/cross_genome::science - Ebuilds: 1, Testing: 20140822
  Description: Genome scaffolding using cross-species synteny
  Homepage: https://www.sanger.ac.uk/tool/crossgenome/
  License: GPL-3+
• sci-biology/cutadapt::science - Ebuilds: 1, Testing: 4.9
  Description: Adapter trimming and other preprocessing of high-throughput sequencing reads
  Homepage: https://github.com/marcelm/cutadapt/
  License: MIT
• sci-biology/dargcc_bidsdata::science - Ebuilds: 1, Testing: 1.0
  Description: BIDS data selection encompassing the wildtype mouse group form the "Dysfunctional Autism Risk Genes Cause Circuit-Specific Connectivity Deficits With Distinct Developmental Trajectories" publication, with DOI: 10.1093/cercor/bhy046 .
  Homepage: https://academic.oup.com/cercor/article/28/7/2495/4975475
  License: GPL-3
• sci-biology/dcm2niix::science - Ebuilds: 1, Testing: 1.0.20210317
  Description: dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. ICOM provides many ways to store/compress image data, known as transfer syntaxes.
  Homepage: https://github.com/rordenlab/dcm2niix
  License: BSD
• sci-biology/dcmstack::science - Ebuilds: 1, Testing: 0.9
  Description: DICOM to Nifti coversion
  Homepage: https://dcmstack.readthedocs.org/en/latest/
  License: MIT
• sci-biology/deeptools::science - Ebuilds: 1, Testing: 3.5.6
  Description: Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig
  Homepage: https://github.com/deeptools/deepTools
  License: BSD
• sci-biology/deeptools-intervals::science - Ebuilds: 1, Testing: 0.1.9-r1
  Description: Constructing interval trees with associated exon/annotation information
  Homepage: https://github.com/deeptools/deeptools_intervals
  License: MIT
• sci-biology/diamond::science - Ebuilds: 1, Testing: 2.0.6
  Description: Alternative of blastp/blastx searches using DNA short reads through protein db
  Homepage: http://ab.inf.uni-tuebingen.de/software/diamond https://github.com/bbuchfink/diamond
  License: AGPL-3
• sci-biology/dipy::science - Ebuilds: 1, Testing: 1.1.1-r1
  Description: Dipy is a free and open source software project for computational neuroanatomy, focusing mainly on diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for denoising, registration, reconstruction, tracking, clustering, visualization, and statistical analysis of MRI data.
  Homepage: https://github.com/nipy/dipy
  License: BSD
• sci-biology/drlfom_bidsdata::science - Ebuilds: 1, Testing: 1.1
  Description: BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center and first associated with the DRLFOM publication. The data represents optp-fMRI mouse brain scans with CBV contrast, tracking serotonergic stimulation over the course of a fluoxetine drinking water treatment.
  Homepage: https://chymera.eu/docs/focus/open-science/
  License: CC-BY-SA-4.0
• sci-biology/edena::science - Ebuilds: 1, Testing: 3.131028
  Description: De novo short read OLC assembler (overlap-layout-consensus)
  Homepage: http://www.genomic.ch/edena.php
  License: GPL-3
• sci-biology/epga::science - Ebuilds: 1, Snapshot: 9999
  Description: De novo assembler using distribution of reads and insert size
  Homepage: https://github.com/bioinfomaticsCSU/EPGA
  License: GPL-3+
• sci-biology/erpin::science - Ebuilds: 1, Testing: 5.5b
  Description: Easy RNA Profile IdentificatioN, an RNA motif search program
  Homepage: http://rna.igmors.u-psud.fr
  License: all-rights-reserved
• sci-biology/exonerate-gff3::science - Ebuilds: 1, Snapshot: 9999
  Description: exonerate-2.2.0 with patches to add GFF3 formatted output
  Homepage: https://github.com/hotdogee/exonerate-gff3
  License: GPL-3
• sci-biology/fastdnaml::science - Ebuilds: 1, Testing: 1.2.2_p10
  Description: Maximum likelihood phylogenetic tree builder for DNA sequences
  Homepage: https://directory.fsf.org/wiki/FastDNAml
  License: GPL-2
• sci-biology/fastp::science - Ebuilds: 1, Testing: 1.3.3
  Description: An ultra-fast all-in-one FASTQ preprocessor
  Homepage: https://github.com/OpenGene/fastp
  License: MIT
• sci-biology/fastqc::science - Ebuilds: 1, Testing: 0.11.9
  Description: Quality control FASTA/FASTQ sequence files
  Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  License: GPL-3+
• sci-biology/ffindex::science - Ebuilds: 1, Testing: 1.0
  Description: Simple index/database for huge amounts of small files
  Homepage: https://github.com/ahcm/ffindex
  License: CC-BY-3.0
• sci-biology/flexbar::science - Ebuilds: 1, Testing: 3.5.0
  Description: Barcode, MID tag and adapter sequence removal
  Homepage: https://github.com/seqan/flexbar
  License: GPL-3
• sci-biology/freebayes::science - Ebuilds: 1, Testing: 1.3.5
  Description: Bayesian gen. variant detector to find short polymorphisms
  Homepage: https://github.com/ekg/freebayes
  License: MIT
• sci-biology/fsa::science - Ebuilds: 1, Testing: 1.15.9
  Description: Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot
  Homepage: https://fsa.sourceforge.net
  License: GPL-3+
• sci-biology/fsl::science - Ebuilds: 2, Testing: 6.0.4
  Description: Analysis of functional, structural, and diffusion MRI brain imaging data
  Homepage: https://www.fmrib.ox.ac.uk/fsl
  License: FSL BSD-2 newmat
• sci-biology/genepop::science - Ebuilds: 1, Testing: 4.7
  Description: Population genetics analysis
  Homepage: https://genepop.curtin.edu.au/ https://kimura.univ-montp2.fr/~rousset/Genepop.htm
  License: CeCILL-2
• sci-biology/genomeview-bin::science - Ebuilds: 1, Testing: 2450-r1
  Description: Genome browser and annotation tool
  Homepage: https://genomeview.sourceforge.net
  License: GPL-2
• sci-biology/germline::science - Ebuilds: 1, Testing: 1.5.3
  Description: Find shared segments of Identity by Descent (IBD) between pairs of individuals
  Homepage: http://gusevlab.org/projects/germline/ http://genome.cshlp.org/content/19/2/318.full
  License: GPL-2
• sci-biology/gffcompare::science - Ebuilds: 1, Testing: 0.12.2
  Description: Compare, classify, merge, track, annotate GFF files
  Homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml https://github.com/gpertea/gffcompare
  License: MIT Artistic-2
• sci-biology/gffread::science - Ebuilds: 1, Testing: 0.12.7
  Description: GFF/GTF utility providing format conversions, filter/extract regions from FASTA
  Homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml https://github.com/gpertea/gffread
  License: MIT
• sci-biology/gffutils::science - Ebuilds: 1, Testing: 0.14
  Description: GFF and GTF file manipulation and interconversion
  Homepage: https://gffutils.readthedocs.io/en/latest/
  License: MIT
• sci-biology/glean::science - Ebuilds: 1, Testing: 1.0.1
  Description: Merge various gene prediction into one (unsupervised learning system)
  Homepage: https://sourceforge.net/projects/glean-gene/
  License: Artistic
• sci-biology/grabix::science - Ebuilds: 1, Snapshot: 9999
  Description: Provide random access to text files BGZF compressed with bgzip
  Homepage: https://github.com/arq5x/grabix
  License: MIT
• sci-biology/graf-bin::science - Ebuilds: 1, Testing: 2.4
  Description: Find closely related subjects using SNP genotype data, validate pedigree file
  Homepage: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi
  License: public-domain
• sci-biology/grappa::science - Ebuilds: 1, Testing: 2.0
  Description: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
  Homepage: https://www.cs.unm.edu/~moret/GRAPPA/
  License: GPL-2
• sci-biology/hexamer::science - Ebuilds: 1, Testing: 19990330
  Description: Predict CDS using 6mers without deriving information from base composition
  Homepage: http://www.sanger.ac.uk/resources/software
  License: all-rights-reserved
• sci-biology/hisat2::science - Ebuilds: 1, Testing: 2.2.1
  Description: Align DNA reads to a population of genomes
  Homepage: https://daehwankimlab.github.io/hisat2 https://github.com/DaehwanKimLab/hisat2
  License: GPL-3+
• sci-biology/idba::science - Ebuilds: 2, Testing: 1.1.3, Snapshot: 9999
  Description: De novo De Bruijn graph assembler iteratively using multimple k-mers
  Homepage: https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/
  License: GPL-2+
• sci-biology/imagej::science - Ebuilds: 2, Testing: 1.54i-r1, Snapshot: 9999
  Description: Image Processing and Analysis in Java
  Homepage: https://imagej.net/software/imagej/ https://github.com/imagej
  License: public-domain
• sci-biology/irsabi_bidsdata::science - Ebuilds: 1, Testing: 1.4
  Description: BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center and first associated with the IRSABI publication. The data represents f/MRI mouse brain scans with both BOLD and CBV contrasts, and acquired during optogenetic stimulation over multiple sessions including acute (i.v.) and chronic (s.c.) fluoxetine administration sessions.
  Homepage: https://chymera.eu/docs/focus/open-science/
  License: CC-BY-SA-4.0
• sci-biology/jannovar-bin::science - Ebuilds: 1, Testing: 0.35
  Description: Exome annotation tool (upstream jar binaries)
  Homepage: https://jannovar.readthedocs.io/en/master/
  License: BSD-2
• sci-biology/jellyfish::science - Ebuilds: 2, Testing: 2.3.0
  Description: k-mer counter within reads for assemblies
  Homepage: https://genome.umd.edu/jellyfish.html
  License: GPL-3+ BSD
• sci-biology/jtreeview-bin::science - Ebuilds: 1, Testing: 1.2.0
  Description: Viewer for Microarray Data in PCL or CDT formats
  Homepage: https://jtreeview.sourceforge.net/
  License: GPL-2
• sci-biology/karect::science - Ebuilds: 1, Testing: 1.0
  Description: Error-correct mismatches and InDels of raw reads incl. paired-end
  Homepage: https://github.com/aminallam/karect http://bioinformatics.oxfordjournals.org/content/31/21/3421.abstract
  License: GPL-2
• sci-biology/lastz::science - Ebuilds: 1, Testing: 1.04.03
  Description: A pairwise DNA sequence aligner, a BLASTZ replacement
  Homepage: http://www.bx.psu.edu/~rsharris/lastz/
  License: all-rights-reserved
• sci-biology/lemur-brain-atlas::science - Ebuilds: 1, Testing: 0.1
  Description: MRI template and 120-region atlas for the mouse lemur primate Microcebus murinus. Generated from 34 animals aged 15-58 months old scanned at 7T using a T2-weighted sequence, resolution 115 × 115 × 230 µm. The template was up-sampled to 91 µm isotropic for hand-segmentation of structures, and also used to create probability maps of grey matter, white matter and cerebro-spinal fluid.
  Homepage: https://www.nitrc.org/projects/mouselemuratlas
  License: CeCILL-2
• sci-biology/libBigWig::science - Ebuilds: 3, Testing: 0.4.7, Snapshot: 9999
  Description: C library for handling bigWig files (functionally replacing Jim Kent's lib)
  Homepage: https://github.com/dpryan79/libBigWig
  License: MIT
• sci-biology/lighter::science - Ebuilds: 2, Testing: 1.1.2, Snapshot: 9999
  Description: NGS reads corrector
  Homepage: https://github.com/mourisl/Lighter
  License: GPL-2+
• sci-biology/lucy::science - Ebuilds: 1, Testing: 1.20
  Description: DNA sequence quality and vector trimming tool
  Homepage: https://lucy.sourceforge.net/
  License: Artistic
• sci-biology/lumpy-sv::science - Ebuilds: 1, Testing: 0.3.1
  Description: Probabilistic framework for structural variant discovery
  Homepage: https://github.com/arq5x/lumpy-sv
  License: MIT
• sci-biology/mappy::science - Ebuilds: 1, Testing: 2.26
  Description: Minimap2 python binding
  Homepage: https://github.com/haotianteng/chiron
  License: MIT
• sci-biology/megahit::science - Ebuilds: 1, Testing: 1.2.9
  Description: Metagenome assembler using succinct de Bruijn graph approach with CUDA
  Homepage: https://github.com/voutcn/megahit http://bioinformatics.oxfordjournals.org/content/31/10/1674.abstract
  License: GPL-3
• sci-biology/merlin::science - Ebuilds: 1, Testing: 1.1.2
  Description: Statistical analysis of gene flow in pedigrees
  Homepage: https://csg.sph.umich.edu/abecasis/Merlin/
  License: merlin
• sci-biology/minimap2::science - Ebuilds: 1, Testing: 2.24-r1
  Description: splice-aware sequence aligner with SSE2 and SSE4.1
  Homepage: https://github.com/lh3/minimap2
  License: MIT
• sci-biology/mip-scaffolder::science - Ebuilds: 1, Testing: 0.6
  Description: Scaffold contigs using ABI Solid or Illumina mate pair info
  Homepage: http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder
  License: BSD-2
• sci-biology/miranda::science - Ebuilds: 1, Testing: 3.3a
  Description: An algorithm for finding genomic targets for microRNAs
  Homepage: https://www.mskcc.org/research/ski/programs/computational-biology
  License: GPL-2
• sci-biology/mmseqs2::science - Ebuilds: 1, Testing: 13.0-r1
  Description: MMseqs2 (Many-against-Many sequence searching) is a software suite toi search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.
  Homepage: https://github.com/soedinglab/MMseqs2
  License: GPL-3
• sci-biology/mouse-brain-templates::science - Ebuilds: 1, Testing: 0.5.3
  Description: A collection of mouse brain templates in NIfTI format
  Homepage: https://github.com/IBT-FMI/mouse-brain-templates_generator
  License: fairuse
• sci-biology/mreps::science - Ebuilds: 1, Testing: 2.6.01
  Description: Identification of serial/tandem repeats in DNA sequences
  Homepage: https://mreps.univ-mlv.fr/
  License: GPL-2
• sci-biology/mrfast::science - Ebuilds: 1, Testing: 2.6.0.1
  Description: Micro Read Fast Alignment Search Tool
  Homepage: http://mrfast.sourceforge.net/
  License: BSD
• sci-biology/msautil::science - Ebuilds: 1, Testing: 1.1-r1
  Description: Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode)
  Homepage: http://bioresearch.byu.edu/msa
  License: all-rights-reserved
• sci-biology/multiqc::science - Ebuilds: 1, Testing: 1.33
  Description: Aggregate bioinformatics results across many samples into a single report
  Homepage: https://multiqc.info/
  License: GPL-3
• sci-biology/nanopolish::science - Ebuilds: 1, Snapshot: 9999
  Description: Signal-level analysis of Oxford Nanopore sequencing data
  Homepage: https://github.com/jts/nanopolish
  License: MIT
• sci-biology/neuroconv::science - Ebuilds: 1, Testing: 0.4.8-r1
  Description: Create NWB files from proprietary formats.
  Homepage: https://github.com/catalystneuro/neuroconv
  License: BSD
• sci-biology/nextclip::science - Ebuilds: 1, Testing: 1.3.1
  Description: Split Illumina Nextera long mate-pairs
  Homepage: https://github.com/richardmleggett/nextclip https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519
  License: GPL-3+
• sci-biology/nitime::science - Ebuilds: 2, Testing: 0.10.2, Snapshot: 9999
  Description: Nitime is a library for time-series analysis of data from neuroscience experiments in both the time and spectral domains.
  Homepage: http://nipy.org/nitime/index.html
  License: BSD
• sci-biology/nrcl::science - Ebuilds: 1, Testing: 110625
  Description: Containment clustering and layout utility for processing pairwise alignments
  Homepage: https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/
  License: Artistic
• sci-biology/ntCard::science - Ebuilds: 2, Testing: 1.2.2, Snapshot: 9999
  Description: Estimate k-mer coverage histogram of genomics data
  Homepage: https://github.com/bcgsc/ntCard
  License: MIT
• sci-biology/nxtrim::science - Ebuilds: 1, Testing: 0.4.3
  Description: Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker
  Homepage: https://github.com/sequencing/NxTrim
  License: BSD-2
• sci-biology/open-ephys-gui::science - Ebuilds: 3, Testing: 0.6.7, Snapshot: 99999999
  Description: Processing, recording, and visualizing multichannel ephys data
  Homepage: https://open-ephys.org/gui/
  License: GPL-3
• sci-biology/opfvta_bidsdata::science - Ebuilds: 1, Testing: 2.0
  Description: BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center and first associated with the OPFVTA publication. The data represents f/MRI mouse brain scans with both BOLD and CBV contrasts, using block and phasic stimulation protocols delivered via a laser to the VTA, which is rendered sensitive by channelrhodopsin expression under the dopamine transporter promoter.
  Homepage: http://chymera.eu/docs/focus/open-science/
  License: CC-BY-SA-4.0
• sci-biology/pairagon::science - Ebuilds: 1, Testing: 1.1
  Description: HMM-based cDNA to genome aligner
  Homepage: https://mblab.wustl.edu/software.html
  License: BSD-2
• sci-biology/parafly::science - Ebuilds: 1, Testing: 0.1.0
  Description: Parallel cmd processing utility
  Homepage: https://github.com/ParaFly/ParaFly
  License: BSD-BroadInstitute
• sci-biology/pbbam::science - Ebuilds: 1, Testing: 2.1.0
  Description: PacBio modified BAM file format
  Homepage: https://pbbam.readthedocs.io/en/latest/index.html
  License: blasr
• sci-biology/pbcopper::science - Ebuilds: 1, Testing: 1.9.5
  Description: Core C++ library for data structures, algorithms, and utilities
  Homepage: https://github.com/PacificBiosciences/pbcopper
  License: blasr
• sci-biology/perga::science - Ebuilds: 1, Snapshot: 9999
  Description: Paired End Reads Guided Assembler
  Homepage: https://github.com/hitbio/PERGA http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252104
  License: all-rights-reserved
• sci-biology/perlprimer::science - Ebuilds: 1, Testing: 1.1.21
  Description: Primers design for standard PCR, bisulphite PCR and Real-time PCR
  Homepage: http://perlprimer.sourceforge.net/
  License: GPL-2
• sci-biology/pileup::science - Ebuilds: 1, Testing: 0.6
  Description: SSAHA2-based pipeline to align reads
  Homepage: https://www.sanger.ac.uk/resources/software/ssaha2/
  License: GRL
• sci-biology/portrait::science - Ebuilds: 1, Testing: 1.1
  Description: Ab initio ncRNA prediction
  Homepage: http://bioinformatics.cenargen.embrapa.br/portrait
  License: GPL-3+
• sci-biology/prinseq-lite::science - Ebuilds: 1, Testing: 0.20.4
  Description: Describe, trim, reformat and convert to or form FASTA/FASTQ files
  Homepage: http://prinseq.sourceforge.net/
  License: GPL-3+
• sci-biology/proda::science - Ebuilds: 1, Testing: 1.0
  Description: Multiple alignment of protein sequences with repeated and shuffled elements
  Homepage: http://proda.stanford.edu/
  License: public-domain
• sci-biology/psx::science - Ebuilds: 1, Testing: 0.1
  Description: parallel multi-FASTA file processing tool from TIGR Gene Indices project tools
  Homepage: https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/
  License: Artistic
• sci-biology/quicktree::science - Ebuilds: 1, Testing: 2.5
  Description: Rapid reconstruction of phylogenies by the Neighbor-Joining method
  Homepage: https://github.com/khowe/quicktree/
  License: Apache-2.0
• sci-biology/rat-brain-templates::science - Ebuilds: 1, Testing: 0.2
  Description: Digital rat brain template collection containing data files in NIfTI format oriented in the standard RAS space, with origin at bregma for use in magnetic resonance rat brain imaging.
  Homepage: https://gitlab.com/FOS-FMI/rat-brain-templates_generator
  License: fairuse
• sci-biology/rnaplex::science - Ebuilds: 1, Testing: 0.2
  Description: RNA-RNA interaction search
  Homepage: http://www.bioinf.uni-leipzig.de/Software/RNAplex/
  License: GPL-2
• sci-biology/roiextractors::science - Ebuilds: 1, Testing: 0.5.1
  Description: Optical imaging data handling from several file formats
  Homepage: https://github.com/catalystneuro/roiextractors
  License: BSD
• sci-biology/sabre::science - Ebuilds: 1, Snapshot: 9999
  Description: Barcode demultiplexing and trimming tool for Illumina FastQ files
  Homepage: https://github.com/najoshi/sabre
  License: MIT
• sci-biology/samri_bidsdata::science - Ebuilds: 1, Testing: 0.3
  Description: BIDS-formatted example mouse brain data for SAMRI
  Homepage: https://github.com/IBT-FMI/SAMRI
  License: GPL-3
• sci-biology/samri_bindata::science - Ebuilds: 1, Testing: 0.4
  Description: ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI
  Homepage: https://github.com/IBT-FMI/SAMRI
  License: GPL-3
• sci-biology/samstat::science - Ebuilds: 1, Testing: 1.5.1
  Description: Statistics of BAM/SAM files
  Homepage: http://samstat.sourceforge.net
  License: GPL-3
• sci-biology/scan_for_matches::science - Ebuilds: 1, Testing: 20121220
  Description: Pattern search through DNA sequences (aka patscan)
  Homepage: https://blog.theseed.org/servers/2010/07/scan-for-matches.html
  License: public-domain
• sci-biology/scythe::science - Ebuilds: 1, Snapshot: 9999
  Description: Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa
  Homepage: https://github.com/vsbuffalo/scythe
  License: MIT
• sci-biology/seqtk::science - Ebuilds: 1, Testing: 1.3
  Description: Manipulate FASTA and FASTQ files
  Homepage: https://github.com/lh3/seqtk
  License: MIT
• sci-biology/seqtools::science - Ebuilds: 1, Testing: 4.44.1
  Description: Display alignments and GFF files, matrix dot plots (blixem, dotter, belvu)
  Homepage: http://www.sanger.ac.uk/resources/software/seqtools
  License: GPL-3
• sci-biology/sff_dump::science - Ebuilds: 1, Testing: 1.04
  Description: Convert Roche SFF files to FASTA file format
  Homepage: http://genome.imb-jena.de/software/roche454ace2caf
  License: FLI-Jena
• sci-biology/sickle::science - Ebuilds: 2, Testing: 1.33, Snapshot: 9999
  Description: Windowed adaptive quality-based trimming tool for FASTQ data
  Homepage: https://github.com/najoshi/sickle
  License: MIT
• sci-biology/skewer-bin::science - Ebuilds: 1, Testing: 0.2.2
  Description: Adaptor and MID removal / trimming tool
  Homepage: https://sourceforge.net/projects/skewer
  License: Artistic
• sci-biology/smalt::science - Ebuilds: 1, Testing: 0.7.6
  Description: DNA read mapper using k=20 (successor of ssaha2)
  Homepage: https://sourceforge.net/projects/smalt/
  License: GPL-3
• sci-biology/smalt-bin::science - Ebuilds: 1, Testing: 0.7.6
  Description: Pairwise sequence alignment mapping DNA reads onto genomic reference
  Homepage: https://sourceforge.net/projects/smalt/
  License: all-rights-reserved
• sci-biology/snap::science - Ebuilds: 1, Testing: 20131129
  Description: HMM-based prokaryotic and eukaryotic gene prediction tool
  Homepage: http://korflab.ucdavis.edu/software.html
  License: MIT
• sci-biology/snapgene::science - Ebuilds: 2, Testing: 8.2.2
  Description: Software for plasmid mapping, primer design, and restriction site analysis
  Homepage: https://www.snapgene.com/snapgene-viewer
  License: snapgene
• sci-biology/snpomatic::science - Ebuilds: 1, Testing: 1.0
  Description: Stringent short-read aligner supporting filters and various output formats
  Homepage: https://github.com/magnusmanske/snpomatic
  License: GPL-3
• sci-biology/spm::science - Ebuilds: 1, Testing: 12_p7771
  Description: Analysis of brain imaging data sequences for Octave or Matlab
  Homepage: https://www.fil.ion.ucl.ac.uk/spm/
  License: GPL-2+
• sci-biology/sra-tools::science - Ebuilds: 1
  Description: NCBI Sequence Read Archive (SRA) sratoolkit
  Homepage: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools
  License: public-domain
• sci-biology/ssaha2-bin::science - Ebuilds: 1, Testing: 2.5.5-r1
  Description: SSAHA2: Sequence Search and Alignment by Hashing Algorithm
  Homepage: https://www.sanger.ac.uk/tool/ssaha2-0/
  License: all-rights-reserved
• sci-biology/stacks::science - Ebuilds: 1, Testing: 2.60
  Description: Analyze restriction enzyme data, draw gen. maps, population genomics
  Homepage: http://creskolab.uoregon.edu/stacks
  License: GPL-3
• sci-biology/stringtie::science - Ebuilds: 1, Testing: 2.1.5
  Description: Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks
  Homepage: https://ccb.jhu.edu/software/stringtie https://github.com/gpertea/stringtie
  License: Artistic-2 MIT
• sci-biology/subread::science - Ebuilds: 1, Testing: 2.0.3
  Description: NGS suite for analysis of mapped reads, summary of exon/intron/gene counts
  Homepage: http://bioinf.wehi.edu.au/featureCounts/
  License: GPL-3
• sci-biology/swissknife::science - Ebuilds: 1, Testing: 1.80
  Description: Perl library of modules to manipulate SwissProt flatfiles
  Homepage: http://swissknife.sourceforge.net/
  License: GPL-2+
• sci-biology/tabixpp::science - Ebuilds: 1, Testing: 1.1.0
  Description: C++ wrapper to tabix indexer
  Homepage: https://github.com/ekg/tabixpp
  License: MIT
• sci-biology/tagdust::science - Ebuilds: 1, Testing: 20101028
  Description: Trim multimers of various primers/adapter from Illumina datasets
  Homepage: http://genome.gsc.riken.jp/osc/english/dataresource
  License: GPL-3
• sci-biology/tigr-foundation-libs::science - Ebuilds: 1, Testing: 2.0-r2
  Description: TIGR Foundation for C++
  Homepage: https://sourceforge.net/projects/amos/
  License: Artistic
• sci-biology/trf-bin::science - Ebuilds: 1, Testing: 4.09
  Description: Tandem Repeats Finder
  Homepage: http://tandem.bu.edu/trf/trf.html
  License: trf
• sci-biology/trimmomatic::science - Ebuilds: 1, Testing: 0.39
  Description: Illumina adapter trimming tool
  Homepage: http://www.usadellab.org/cms/?page=trimmomatic
  License: GPL-3
• sci-biology/trinityrnaseq::science - Ebuilds: 1, Testing: 2.13.2
  Description: Transcriptome assembler for RNA-seq reads
  Homepage: https://github.com/Trinotate/Trinotate.github.io/wiki
  License: BSD-BroadInstitute
• sci-biology/twinscan::science - Ebuilds: 1, Testing: 4.1.2-r1
  Description: iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline
  Homepage: https://mblab.wustl.edu/software.html
  License: all-rights-reserved
• sci-biology/ugene::science - Ebuilds: 1, Testing: 40.1-r1
  Description: A free open-source cross-platform bioinformatics software
  Homepage: http://ugene.unipro.ru
  License: GPL-2
• sci-biology/vague-bin::science - Ebuilds: 1, Testing: 1.0.5
  Description: GUI for Velvet de novo assembler
  Homepage: https://vicbioinformatics.com/software.vague.shtml
  License: GPL-2
• sci-biology/vcflib::science - Ebuilds: 1
  Description: VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)
  Homepage: https://github.com/vcflib/vcflib
  License: MIT-with-advertising
• sci-biology/verifyBamID::science - Ebuilds: 1, Testing: 1.1.3
  Description: Verify sample identity/mix and genotype concordance
  Homepage: http://genome.sph.umich.edu/wiki/VerifyBamID
  License: GPL-3+
• sci-biology/vt::science - Ebuilds: 1, Snapshot: 9999
  Description: A tool set for short variant discovery in genetic sequence data
  Homepage: https://github.com/atks/vt http://genome.sph.umich.edu/wiki/vt
  License: MIT
• sci-biology/wgs_tools::science - Ebuilds: 1, Snapshot: 9999
  Description: Scripts for ncbi-tools++ and SRA postprocessing using taxonomy
  Homepage: ftp://ftp.ncbi.nih.gov/blast/WGS_TOOLS https://www.ncbi.nlm.nih.gov/books/NBK279690/ https://www.ncbi.nlm.nih.gov/genbank/wgs
  License: all-rights-reserved
• sci-biology/yaha::science - Ebuilds: 1, Snapshot: 9999
  Description: DNA mapper for single-end reads to detect structural variants (SV)
  Homepage: https://github.com/GregoryFaust/yaha
  License: MIT
• sci-biology/zmap::science - Ebuilds: 1, Testing: 2.12.0
  Description: A desktop genome browser using GFF inputs
  Homepage: https://www.sanger.ac.uk/science/tools/zmap
  License: GPL-2
• sci-biology/zmsort::science - Ebuilds: 1, Testing: 110625
  Description: Merge-sort utility for compressed alignment files, with multi-file output
  Homepage: https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/
  License: Artistic