Ycarus Gentoo ebuild

science

These ebuilds come from .

If you have some problems, go to the official site first.

sci-biology

ANGLE-bin : CDS prediction overcoming sequencing errors in unfinished cDNA ( http://bioinformatics.cenargen.embrapa.br/portrait/download )

AlignGraph : Reference-genome-assisted asssembly of contigs/scaffolds using PE reads ( https://github.com/baoe/AlignGrap )

Atlas : Atlas Whole Genome Assembly Suite ( https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite )

Atlas-Link : Link and orient genome sequence contigs using mate-pair information ( https://www.hgsc.bcm.edu/software/atlas-link )

Atlas2 : Variant analysis tools from whole exome capture sequencing (WECS) ( https://www.hgsc.bcm.edu/software/atlas2 )

Atlas_GapFill : Close gaps using BWA-identified reads and reassemble ( https://www.hgsc.bcm.edu/software/atlas-gapfill )

BBmap : Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool ( http://sourceforge.net/projects/bbmap/ )

BG7 : Bacterial genome annotation system ( http://bg7.ohnosequences.com )

BRAKER : Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS ( http://bioinf.uni-greifswald.de/bioinf/brake )

BRANCH : Extend partial transcripts with sequence from other reads or genomic contigs ( https://github.com/baoe/BRANCH )

BamView : Display read alignments in BAM files, is a part of Artemis ( http://bamview.sourceforge.net/ )

BlastToSam : Convert NCBI BLAST+ Pairwise/XML (-outfmt 0 or 5) output to SAM v1.4 ( https://github.com/AstrorEnales/BlastToSam )

DisEMBL : Intrinsic Protein Disorder Prediction ( http://dis.embl.de )

EBARDenovo : Transcriptome de novo assembler with chimera detection ( http://ebardenovo.sourceforge.net )

ESTate : ORF finding despite frameshifts, EST clustering ( http://www.ebi.ac.uk/~guy/estate )

FLASH : Paired-end mates merge from fragments ( http://sourceforge.net/projects/flashpage )

Fastaq : Manipulate FASTA/Q, GFF3, EMBL, GBK files with API for developers ( https://github.com/sanger-pathogens/Fastaq )

GAL : Genome Annotation Library (incl. fasta_tool) ( http://www.sequenceontology.org/software/GAL.html )

Gambit : Genomic alignments from BAM files ( http://code.google.com/p/gambit-viewer/ )

ICC : Error corrector for Roche/454 and IonTorrent data ( http://indra.mullins.microbiol.washington.edu/ICC )

IMAGE : Iterative Mapping and Assembly for Gap Elimination using paired-end Illumina ( https://sourceforge.net/apps/mediawiki/image2 )

InterMine : Biological data warehouse integrating complex data ( http://github.com/intermine/intermine )

KING : Check family relationship and infer population structure ( http://people.virginia.edu/~wc9c/KIN )

KaKs_Calculator : Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates ( https://code.google.com/p/kaks-calculator )

MaSuRCA : de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore ( http://www.genome.umd.edu/masurca.htm )

MagicViewer : Display short reads alignment ( http://bioinformatics.zj.cn/magicviewer )

MeV : Multiple experiment Viewer for genomic data analysis ( http://mev-tm4.sourceforge.net )

MochiView : Genome browser and analysis ( http://johnsonlab.ucsf.edu/mochi.html )

MolBioLib : C++11 framework for rapid develop and deploy of bioinformatic tasks ( https://sourceforge.net/projects/molbiolib )

MuSeqBox : Parse and filter BLAST output into tab-delimited file ( http://brendelgroup.org/bioinformatics2go/MuSeqBox.php )

NGSTools : Next Generation Sequencing Eclipse Plugin (CNV and indel discovery), aka NGSEP ( https://sourceforge.net/p/ngsep/wiki/Home )

OBO-Edit : Java-based editor optimized for the OBO biological ontology file format ( http://www.oboedit.org/ )

ONTO-PERL : Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology) ( )

ORFcor : Automated editor of protein-coding sequences ( http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058387 )

RADtools : Tools for processing RAD Sequencing Illumina reads ( https://www.wiki.ed.ac.uk/display/RADSequencing/Home )

RSeQC : Utilities for RNA-seq data quality control ( http://rseqc.sourceforge.net )

Ray : Assembler for metagenomes, genomes and transcriptomes using MPI ( http://denovoassembler.sourceforge.net/ )

Rcorrector : Error correction for Illumina RNA-seq reads ( https://github.com/mourisl/Rcorrector )

SEECER : SEquence Error Corrector for RNA-Seq reads ( http://sb.cs.cmu.edu/seecer/ )

SOAPdenovo2 : Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT) ( https://github.com/aquaskyline/SOAPdenovo )

SPAdes : De novo de Bruijn genome assembler overcoming uneven coverage ( http://cab.spbu.ru/software/spades )

SSAKE : Short-read trimmer, OLC assembler, scaffolder in PERL using the 3'-most k-mers ( http://www.bcgsc.ca/platform/bioinfo/software/ssake )

STAR : STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays ( http://code.google.com/p/rna-star/ )

Scaffolder-evaluation : Scripts to run genome assembly scaffolding tools and analyse output for accuracy ( https://github.com/martinghunt/Scaffolder-evaluatio )

Sibelia : Draw synteny plots using circos ( http://bioinf.spbau.ru/en/sibelia )

SnpEff : SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF ( http://snpeff.sourceforge.net )

SolexaQA : Analyze and trim single-end and paired-end reads, show quality statistics ( http://sourceforge.net/projects/clview )

StarORF : Java-based utility to show ORFs in a sequence ( http://star.mit.edu/orf )

TransDecoder : Extract ORF/CDS regions from FASTA sequences ( http://transdecoder.github.io )

Trinotate : Annotation and analysis pipeline for de novo assembled transcriptomes ( http://trinotate.github.io )

VarScan : Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls) ( http://varscan.sourceforge.net/ )

VarScan-bin : Variant detection (germline, multi-sample, somatic mut., CNA), SNP ( http://dkoboldt.github.io/varscan )

VelvetOptimiser : Optimise Velvet sequence assembler ( http://www.vicbioinformatics.com/software.velvetoptimiser.shtml )

YASRA : Yet Another Short Read Assembler aligning to a reference using LASTZ ( http://www.bx.psu.edu/miller_lab/ )

abacas : Order and orientate DNA contigs even via 6-frame protein alignments ( http://abacas.sourceforge.net )

act-bin : DNA contig sequence comparison tool supplementing Artemis ( http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act )

afni : An open-source environment for processing and displaying functional MRI data ( http://afni.nimh.nih.gov/ )

aghermann : A sleep-research experiment manager, EDF viewer and Process S simulator ( http://johnhommer.com/academic/code/aghermann )

align_to_scf : View trace information at a given position missing from Roche .ace files ( http://genome.imb-jena.de/software/roche454ace2caf )

amos : Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies ( http://sourceforge.net/projects/amos )

ampliconnoise : Noise removal from pyrosequenced amplicons ( http://code.google.com/p/ampliconnoise/ )

angsd : Population genetics analysis package ( http://www.popgen.dk/angsd )

ants : Advanced Normalitazion Tools for neuroimaging ( http://stnava.github.io/ANTs/ )

apollo : Apollo genome editor ( http://gmod.org/wiki/Apollo )

arachne : Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig) ( https://www.broadinstitute.org/crd/wik )

argo : Production tool for visualizing and manually annotating whole genomes ( http://www.broadinstitute.org/annotation/argo )

argo-bin : Visualization and manually annotating whole genomes ( http://www.broadinstitute.org/annotation/argo )

artemis : DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool ( http://www.sanger.ac.uk/resources/software/artemis )

assembly-stats : Assembly statistics (min, max, sum, N50, N90, count gaps and Ns) ( https://github.com/martinghunt/assembly-stats )

atsas : Biological Small Angle Scattering ( http://www.embl-hamburg.de/biosaxs )

augustus : Eukaryotic gene predictor ( http://augustus.gobics.de/ )

autoeditor : Automatic correct of discrepancies in multiple sequence alignments ( http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor )

bam-readcount : Count DNA sequence reads in BAM files and other statistics calculations ( https://github.com/genome/bam-readcount )

bambino : display SAM/BAM files and for SNP/indel detection, report coverage in .wig files ( https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html einfo "More info at "${HOMEPAGE )

bambus : Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle ( HOMEPAGE=" )

bamql : Extract reads from BAM files ( https://github.com/BoutrosLaboratory/bamq )

barnacle : Check de novo assembly for chimeric contigs/transcripts ( http://www.bcgsc.ca/platform/bioinfo/software/barnacle )

barrnap : Predict Bacterial and Archaeal rRNA genes and output in GFF3 format ( http://www.vicbioinformatics.com/software.barrnap.shtml )

beagle : Genotype calling/phasing, imputation of ungenotyped markers ( http://faculty.washington.edu/browning/beagle/beagle.html )

beaglecall : Simultaneous genotype calling and haplotype phasing for unrelated individuals ( http://faculty.washington.edu/browning/beaglecall/beaglecall.html )

bedops : Manipulate BED file (alternative to bedtools) ( http://bedops.readthedocs.i )

bfast : Blat-like Fast Accurate Search Tool (short read mapper) ( https://sourceforge.net/projects/bfast )

bio-cd-hit-report : Ruby library for reading CD-HIT cluster reports ( https://rubygems.org/gems/bio-cd-hit-report )

biobambam : Tools for bam file processing ( https://github.com/gt1/biobambam )

biobambam2 : Tools for bam file processing (libmaus2) ( https://github.com/gt1/biobambam2 )

biopieces : Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank ( http://code.google.com/p/biopieces )

bismark : Map bisulfite converted sequence reads and cytosine methylation states ( http://www.bioinformatics.babraham.ac.uk/projects/bismark/ )

blasr : The PacBio long read aligner ( http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR )

blat : The BLAST-Like Alignment Tool, a fast genomic sequence aligner ( http://www.cse.ucsc.edu/~kent/ )

blue : Error corrector for Illummina and Roche/454, including insertions and deletions ( http://www.bioinformatics.csiro.au/blue )

brat : Bisulfite-treated Reads Analysis Tool (short read mapper) ( http://compbio.cs.ucr.edu/brat/ )

brat_bw : Bisulfite-aware short read mapper, FM-index, no InDel support ( http://compbio.cs.ucr.edu/brat/ )

brat_nova : Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align ( http://compbio.cs.ucr.edu/brat/ )

breakdancer : Genome-wide detection of structural variants from paired-end sequencing reads ( http://gmt.genome.wustl.edu/packages/breakdancer )

bru2nii : Converts Bruker ParaVision MRI data to the NIfTI file format ( https://github.com/neurolabusc/Bru2Nii )

bwa : Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner ( http://bio-bwa.sourceforge.net/ )

bx-python : Library for rapid implementation of genome scale analyses ( https://bitbucket.org/james_taylor/bx-python/wiki/Home )

caftools : Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP ( http://www.sanger.ac.uk/resources/software/ca )

cast-bin : Predict low-complexity regions in putative proteins ( http://bioinformatics.cenargen.embrapa.br/portrait/download )

cd-hit : Clustering Database at High Identity with Tolerance ( http://weizhong-lab.ucsd.edu/cd-hi )

cd-hit-auxtools : Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup ( http://weizhong-lab.ucsd.edu/cd-hit/ )

cdbfasta : FASTA record indexing/retrievieng utility ( http://compbio.dfci.harvard.edu/tgi/software )

cegma : Predict genes in a genome and use them for training to find all genes ( http://korflab.ucdavis.edu/datasets/cegma )

cg-cat : r2cat and treecat, scaffolding tools for ordering and orienting contigs ( http://bibiserv.techfak.uni-bielefeld.de/cgcat )

cgview-bin : CGView Comparison Tool to compare genome sequences graphically (aka CCT) ( http://stothard.afns.ualberta.ca/downloads/CCT )

chiron : Basecaller for OxfordNanopore data using deep learning ( https://github.com/haotianteng/chiro )

clover : Cis-eLement OVERrepresentation: Detection of functional DNA motifs ( http://zlab.bu.edu/clover/ )

cluster : Hierarchical, k-means, k-medians clustering for expression/microarray analysis ( http://bonsai.hgc.jp/~mdehoon/software/cluster einfo "Please obtain ${P}.tar.gz from ${HOMEPAGE} and place it in ${DISTDIR} )

clview : clview is an assembly .ace file viewer from TIGR Gene Indices project tools ( http://sourceforge.net/projects/clview )

cnrun : A NeuroML-enabled, precise but slow neuronal network simulator ( http://johnhommer.com/academic/code/cnrun )

codonw : Multivariate statistical analysis of codon and amino acid usage ( http://codonw.sourceforge.net/ )

conform-gt : Modify your Variant Call Format file to be consistent with reference VCF ( http://faculty.washington.edu/browning/conform-gt.html )

conifer : Copy Number Inference/Variants (CNV) from exome reads ( http://conifer.sf.net )

conrad : Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor ( http://www.broadinstitute.org/annotation/conra )

consed2gap : Convert whole CONSED dataset to a GAP4 project ( http://genome.imb-jena.de/software/consed2gap/ )

coral : Error corrector for Illumina and Roche/454 reads using multiple alignment info ( http://www.cs.helsinki.fi/u/lmsalmel/coral )

cortex_var : Genotype variant discovery without reference sequence ( http://cortexassembler.sourceforge.net/index_cortex_var.html )

cramtools : Java tools and APIs for efficient compression of sequence read data ( http://www.ebi.ac.uk/ena/software/cram-toolki )

cross_genome : Genome scaffolding using cross-species synteny ( http://www.sanger.ac.uk/science/tools/crossgenome )

cutadapt : Remove adapter sequences from high-throughput sequencing data ( https://github.com/marcelm/cutadapt )

dawg : DNA Assembly With Gaps: Phylogenetic aligner for sequence evolution simulation ( http://scit.us/projects/dawg/ )

dcmstack : DICOM to Nifti coversion ( https://dcmstack.readthedocs.org/en/latest/ )

deeptools : Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig ( https://github.com/fidelram/deepTools )

diamond : Alternative of blastp/blastx searches using DNA short reads through protein db ( http://ab.inf.uni-tuebingen.de/software/diamon )

dipy : Computational neuroanatomy project focusing on diffusion MRI ( http://nipy.org/dipy )

discrover : A sequence motif discovery tool that uses discriminative learning ( https://github.com/maaskola/discrover )

dna2pep : Translate DNA sequence into protein (with STOP codon read-through) ( http://www.cbs.dtu.dk/services/VirtualRibosome/download.php )

ePCR : Search for sub-sequences matching PCR primers ( http://www.ncbi.nlm.nih.gov/tools/epcr/ )

edena : De novo short read OLC assembler (overlap-layout-consensus) ( http://www.genomic.ch/edena.php )

ensembl-tools : Variant Effect Predictor (VEP), AssemblyMapper, IDMapper, RegionReporter tools ( http://www.ensembl.org/info/docs/tools/vep/scrip )

epga : De novo assembler using distribution of reads and insert size ( https://github.com/bioinfomaticsCSU/EPGA )

erpin : Easy RNA Profile IdentificatioN, an RNA motif search program ( http://tagc.univ-mrs.fr/erpin/ )

est2assembly : EST assembly and annotation pipeline for chado/gbrowse2 display ( http://code.google.com/p/est2assembly/ )

estscan : Prediction of coding regions in DNA/RNA sequences ( http://sourceforge.net/projects/estscan/ )

eugene : Prokaryotic and Eukaryotic gene predictor ( http://www.inra.fr/mia/T/EuGene/ )

eval : Validate, compare and draw summary statistics for GTF files ( http://mblab.wustl.edu/software.html )

exomiser-bin : Annotate VCF files and prioritize genome/exome mutations ( http://www.sanger.ac.uk/science/tools/exomiser )

exonerate-gff3 : exonerate-2.2.0 with patches to add GFF3 formatted output ( https://github.com/hotdogee/exonerate-gff3 )

fastdnaml : Maximum likelihood phylogenetic tree builder for DNA sequences ( http://directory.fsf.org/project/fastDNAml/ )

fastqc : Quality control FASTA/FASTQ sequence files ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ )

ffindex : Simple index/database for huge amounts of small files ( http://www.splashground.de/~andy/programs/FFindex )

fgap : Tool to close gaps in de novo assembled contigs or scaffolds ( http://www.bioinfo.ufpr.br/fgap )

fgap-bin : Tool to close gaps in de novo assembled contigs or scaffolds ( http://www.bioinfo.ufpr.br/fgap )

flexbar : Barcode, MID tag and adapter sequence removal ( https://github.com/seqan/flexbar )

freebayes : Bayesian gen. variant detector to find short polymorphisms ( https://github.com/ekg/freebayes )

fsa : Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot ( http://fsa.sourceforge.net )

fsl : Analysis of functional, structural, and diffusion MRI brain imaging data ( http://www.fmrib.ox.ac.uk/fsl )

full_lengther_next : Classify assembled transcripts and fix frameshifts in ORFs ( http://www.rubydoc.info/gems/full_lengther_nex )

gap2caf : GAP4 file format to CAF v2 format converter for genomic assembly data ( http://www.sanger.ac.uk/resources/software/caf/ )

gatk : The Genome Analysis Toolkit ( http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit )

gbench : View and analyze genome sequences ( http://www.ncbi.nlm.nih.gov/projects/gbench/ )

gemini : Lightweight VCF to DB framework for disease and population genetics ( https://github.com/arq5x/gemin )

geneid : An ab initio exon/gene finding program ( http://genome.crg.es/software/geneid )

genepop : Population genetics analysis ( https://genepop.curtin.edu.au/ https://kimura.univ-montp2.fr/~rousset/Genepop.htm )

generecon : Disequilibrium gene mapping based on coalescent theory using Bayesian MC methods ( http://www.daimi.au.dk/~mailund/GeneRecon/ )

genometools : Tools for bioinformatics (Tallymer, Readjoiner, gff3validator, ...) ( http://genometools.org )

genomeview-bin : Genome browser and annotation tool ( http://genomeview.sourceforge.net )

germline : Find shared segments of Identity by Descent (IBD) between pairs of individuals ( http://www.cs.columbia.edu/~gusev/germlin )

gffcompare : Compare, classify, merge, track, annotate GFF files ( http://ccb.jhu.edu/software/stringtie/gff.shtm )

gffread : GFF/GTF utility providing format conversions, filter/extract regions from FASTA ( http://ccb.jhu.edu/software/stringtie/gff.shtm )

gfftools : gff2ps can render features annotated in GFF file format into PostScript figures ( http://genome.crg.es/software/gfftools/GFF2PS.html )

gffutils : GFF and GTF file manipulation and interconversion ( https://pythonhosted.org/gffutils/ )

glean : Merge various gene prediction into one (unsupervised learning system) ( http://sourceforge.net/projects/glean-gene )

gmap : DNA and splice-aware RNA/cDNA read aligners/mappers (gmap and gsnap) ( http://research-pub.gene.com/gmap/ )

grabix : Provide random access to text files BGZF compressed with bgzip ( https://github.com/arq5x/grabix )

graf-bin : Find closely related subjects using SNP genotype data, validate pedigree file ( http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi )

grappa : Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms ( http://www.cs.unm.edu/~moret/GRAPPA/ )

grass : Scaffold next-generation sequencing assemblies ( https://github.com/AlexeyG/GRASS )

hexamer : Predict CDS using 6mers without deriving information from base composition ( http://www.sanger.ac.uk/resources/software )

hisat2 : Align DNA reads to a population of genomes ( HOMEPAGE=" )

hts-python : Pythonic wrapper for htslib C-API using python cffi (unlike pysam) ( https://github.com/brentp/hts-python )

hydra-sv : Detection of structural variation breakpoints ( http://code.google.com/p/hydra-sv/ )

idba : De novo De Bruijn graph assembler iteratively using multimple k-mers ( http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud )

igv : Integrative Genomics Viewer ( http://www.broadinstitute.org/igv/ )

imagej : Image Processing and Analysis in Java ( http://rsb.info.nih.gov/ij/ )

jannovar : Exome annotation tool ( http://compbio.charite.de/contao/index.php/jannovar.html )

jannovar-bin : Exome annotation tool (upstream jar binaries) ( http://compbio.charite.d )

jellyfish : k-mer counter within reads for assemblies ( http://www.genome.umd.edu/jellyfish.html )

jigsaw : Combine results from external gene predictors into final gene models ( http://www.cbcb.umd.edu/software/jigsaw )

jtreeview : Viewer for Microarray Data in PCL or CDT formats ( http://jtreeview.sourceforge.ne )

jtreeview-bin : Viewer for Microarray Data in PCL or CDT formats ( http://jtreeview.sourceforge.net/ )

karect : Error-correct mismatches and InDels of raw reads incl. paired-end ( https://github.com/aminallam/karec )

kat : K-mer Analysis Toolkit (histogram, filter, compare sets, plot) ( https://github.com/TGAC/KAT )

khmer : In-memory K-mer counting in DNA/RNA/protein sequences ( https://github.com/ged-lab/khmer )

kmergenie : Estimate best k-mer length to be used in novo assemblies ( http://kmergenie.bx.psu.edu/ )

kraken : Detect sequencing project contaminants by mapping reads to taxonomic groups ( http://ccb.jhu.edu/software/krake )

last : Genome-scale comparison of biological sequences ( http://last.cbrc.jp/ )

lastz : A pairwise DNA sequence aligner, a BLASTZ replacement ( http://www.bx.psu.edu/~rsharris/lastz/ )

libBigWig : C library for handling bigWig files (functionally replacing Jim Kent's lib) ( https://github.com/dpryan79/libBigWig )

lighter : NGS reads corrector ( https://github.com/mourisl/Lighter )

lucy : DNA sequence quality and vector trimming tool ( http://lucy.sourceforge.net/ )

lumpy-sv : Probabilistic framework for structural variant discovery ( https://github.com/arq5x/lumpy-sv )

mRNAmarkup : Transcript annotation workflow ( http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php )

maker : A genome annotation viewer and pipeline for small eukaryota and prokaryota ( http://www.yandell-lab.org/software/maker.html" einfo "Please visit ${HOMEPAGE} and obtain the file )

manatee-igs : IGS-modified version of the genome annotation tool using Chado database schema ( http://manatee.sourceforge.net/igs )

manatee-jcvi : Genome annotation tool ( http://manatee.sourceforge.net/jcvi/downloads.shtml )

mavid : Multiple alignment of large DNA sequences ( http://baboon.math.berkeley.edu/mavid/ )

megahit : Metagenome assembler using succinct de Bruijn graph approach with CUDA ( https://github.com/voutcn/megahi )

merlin : Statistical analysis of gene flow in pedigrees ( http://www.sph.umich.edu/csg/abecasis/Merlin/ )

metaseq : Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data ( http://pythonhosted.org/metaseq/ )

mgblast : Customized version of megablast from TIGR Gene Indices project ( http://compbio.dfci.harvard.edu/tgi/software/ )

minced : Short Palindromic Repeat finder tool (for CRISPRs) ( https://github.com/ctSkennerton/minced/tree/master )

mip-scaffolder : Scaffold contigs using ABI Solid or Illumina mate pair info ( http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder )

mira : Whole Genome Shotgun and EST Sequence Assembler ( http://www.chevreux.org/projects_mira.html )

miranda : An algorithm for finding genomic targets for microRNAs ( http://www.microrna.org/ )

mne-python : Python package for MEG and EEG data analysis ( http://martinos.org/mne/mne-python.html )

mothur : A suite of algorithms for ecological bioinformatics ( http://www.mothur.org/ )

mouse-brain-atlases : A collection of mouse brain atlases in NIfTI format ( https://github.com/IBT-FMI/mouse-brain-atlases )

mreps : Identification of serial/tandem repeats in DNA sequences ( http://bioinfo.lifl.fr/mreps/ )

mrfast : Micro Read Fast Alignment Search Tool ( http://mrfast.sourceforge.net/ )

mrsfast : Micro Read Fast Alignment Search Tool ( http://mrsfast.sourceforge.net/Home )

msautil : Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode) ( http://bioresearch.byu.edu/msa )

nanopolish : Signal-level analysis of Oxford Nanopore sequencing data ( https://github.com/jts/nanopolish )

ncbi-blast+ : A subset of NCBI C++ Toolkit containing just the NCBI BLAST+ ( http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit )

ncbi-genome-download : Download genomes from the NCBI FTP servers ( https://github.com/kblin/ncbi-genome-download )

ncbi-tools++ : NCBI C++ Toolkit, including NCBI BLAST+ ( http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit )

nesoni : Analysis package for next-generation sequencing data and prepare for IGV display ( http://www.vicbioinformatics.com/software.nesoni.shtml )

nextclip : Split Illumina Nextera long mate-pairs ( https://github.com/richardmleggett/nextcli )

ngs_backbone : Assembly and annotation pipeline with web interface for EST/chromosomal sequences ( http://bioinf.comav.upv.es/ngs_backbone/index.html )

ngsview : Display, edit NGS alignments ( http://sourceforge.net/projects/ngsview )

nilearn : Fast and easy statistical learning on NeuroImaging data ( http://nilearn.github.io/ )

nireg : Image registration package for Python ( http://nipy.org/ )

nistats : Neuroimaging tools for Python ( http://nipy.org/ )

nitime : Time-series analysis of neuroscience data ( http://nipy.org/nitime/index.html )

nrcl : Containment clustering and layout utility for processing pairwise alignments ( http://compbio.dfci.harvard.edu/tgi/software/ )

ntCard : Estimate k-mer coverage histogram of genomics data ( https://github.com/bcgsc/ntCard )

nwalign : Needleman-Wunsch global sequence alignment in python/cython ( https://pypi.python.org/pypi/nwalign )

nxtrim : Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker ( https://github.com/sequencing/NxTrim )

oases : De novo transcriptome assembler ( http://www.ebi.ac.uk/~zerbino/oases )

oncotator : Annotate genetic variants in VCF ( https://github.com/broadinstitute/oncotator )

pairagon : HMM-based cDNA to genome aligner ( http://mblab.wustl.edu/software.html )

parafly : Some dependency for transdecoder ( http://sourceforge.net/projects/transdecoder/ )

pb-honey : Structural variant identification (SNV) using long reads (over 10kbp) ( https://www.hgsc.bcm.edu/software/honey )

pb-jelly : Close gaps using PacBio RS or 454 FLX+ reads ( https://www.hgsc.bcm.edu/software/jelly )

perga : Paired End Reads Guided Assembler ( https://github.com/hitbio/PERG )

perlprimer : Primers design for standard PCR, bisulphite PCR and Real-time PCR ( http://perlprimer.sourceforge.net/ )

phusion : Whole genome shotgun assembler using phrap (for Sanger-based reads) ( http://www.sanger.ac.uk/resources/software/phusion/ )

phusion2 : Whole genome shotgun assembler using phrap (for Sanger-based reads) ( http://www.sanger.ac.uk/resources/software/phusion/ )

picard : Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files ( http://picard.sourceforge.ne )

pileup : SSAHA2-based pipeline to align reads ( http://www.sanger.ac.uk/resources/software/ssaha2/ )

pilon-bin : Fix assembled reference using BAM-aligned reads, call SNPs ( HOMEPAGE=" )

plink : Whole genome association analysis toolset ( http://pngu.mgh.harvard.edu/~purcell/plin )

plinkseq : C/C++ library for working with human genetic variation data ( http://atgu.mgh.harvard.edu/plinkseq )

polyphen : Predict effect of aminoacid substitution on human protein function ( http://genetics.bwh.harvard.edu/pph2/dokuwiki/start )

poretools : Tools for sequencing FAST5 data from Oxford Nanopore ( https://poretools.readthedocs.i )

portrait : Ab initio ncRNA prediction ( http://bioinformatics.cenargen.embrapa.br/portrait )

primerD : Design degenerate primers ( http://mblab.wustl.edu/software.html )

prinseq-lite : Describe, trim, reformat and convert to or form FASTA/FASTQ files ( http://prinseq.sourceforge.net/ )

proda : Multiple alignment of protein sequences with repeated and shuffled elements ( http://proda.stanford.edu/ )

prokka : Prokaryotic whole genome annotation pipeline ( http://www.bioinformatics.net.au/software.prokka.shtml )

proovread : Error correct PacBio subreads using Illumina reads ( https://github.com/BioInf-Wuerzburg/proovread )

prot4EST : Predict proteins from EST sequences overcoming frameshifts ( http://www.compsysbio.org/lab/?q=prot4ES )

psx : parallel multi-FASTA file processing tool from TIGR Gene Indices project tools ( http://compbio.dfci.harvard.edu/tgi/software/ )

psychopy : Python experimental psychology toolkit ( http://www.psychopy.org/ )

pvmsx : Parallel multi-FASTA file processing tool ( http://compbio.dfci.harvard.edu/tgi/software/ )

pybedtools : Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working ( http://pythonhosted.org/pybedtools/ )

pybrain : The Python Machine Learning Library ( http://pybrain.org/ )

pyfaidx : Efficient pythonic random access to fasta subsequences ( https://pypi.python.org/pypi/pyfaidx )

pysamstats : Calculate stats against genome positions from SAM/BAM/CRAM file ( https://github.com/alimanfoo/pysamstat )

pysurfer : Python based program for visualization of data from Freesurfer ( http://pysurfer.github.com )

quast : Compare quality of multiple genome assemblies to each other ( http://bioinf.spbau.ru/QUAST )

quicktree : Rapid reconstruction of phylogenies by the Neighbor-Joining method ( http://www.sanger.ac.uk/Software/analysis/quicktree/ )

quorum : Correct substitution errors in Illumina reads ( http://www.genome.umd.edu/quorum.htm )

reaper : Demultiplex, trim 3'-adapter/polyA and filter short read DNA sequences ( http://www.ebi.ac.uk/~stijn/reaper )

reapr : Verify and correct genome assembly scaffolds using paired-end reads ( http://www.sanger.ac.uk/science/tools/reapr )

repeatmasker : Screen DNA sequences for interspersed repeats and low complexity DNA ( http://repeatmasker.org/ )

repeatmasker-libraries : A special version of RepBase used by RepeatMasker ( http://repeatmasker.org/ )

reptile : Illumina read corrector ( http://aluru-sun.ece.iastate.edu/doku.php?id=reptile )

rmblast : RepeatMasker compatible version of NCBI BLAST+ ${MY_NCBI_BLAST_V} ( http://www.repeatmasker.org/RMBlast.html )

rnaplex : RNA-RNA interaction search ( http://www.bioinf.uni-leipzig.de/Software/RNAplex/ )

roche454ace2caf : ace to gap4 converter ( http://genome.imb-jena.de/software/roche454ace2caf )

rtg-tools : Manipulate and analyze VCF files ( https://github.com/RealTimeGenomics/rtg-tools )

ruffus : Python module to support computational pipelines ( http://www.ruffus.org.uk )

rum : RNA-Seq Unified Mapper (digital normalization) ( https://github.com/itmat/rum/wiki )

sabre : Barcode demultiplexing and trimming tool for Illumina FastQ files ( https://github.com/najoshi/sabre )

sailfish : Rapid Mapping-based Isoform Quantification from RNA-Seq Reads ( http://www.cs.cmu.edu/~ckingsf/software/sailfish/ )

salmon : Transcript-level quantification from RNA-seq reads using lightweight alignments ( https://github.com/COMBINE-lab/salmon )

sambamba : Parallell process SAM/BAM/CRAM files faster than samtools ( http://lomereiter.github.io/sambamba )

samri : Small Animal Magnetic Resonance Imaging ( https://github.com/IBT-FMI/SAMRI )

samri_bindata : Mouse brain atlasses for SAMRI. ( https://github.com/IBT-FMI/SAMRI )

samstat : Statistics of BAM/SAM files ( http://samstat.sourceforge.net )

scaffold_builder : Combine FASTA contigs from a de novo assembly into scaffolds ( HOMEPAGE=" )

scan_for_matches : Pattern search through DNA sequences (aka patscan) ( http://blog.theseed.org/servers/2010/07/scan-for-matches.html )

scbi_blast : Handle blast+ executions using pipes instead of files ( https://rubygems.org/gems/scbi_blast )

scbi_fasta : Read FASTA and QUAL files ( https://rubygems.org/gems/scbi_fasta )

scbi_fastq : Read/write FASTQ files ( https://rubygems.org/gems/scbi_fastq )

scbi_mapreduce : Run parallel and distributed computing jobs ( https://rubygems.org/gems/scbi_mapreduce )

scbi_plot : Wrapper to create plots with gnuplot ( https://rubygems.org/gems/scbi_plot )

scbi_zcat : Read files from a zcat pipe of a gz file ( https://rubygems.org/gems/scbi_zcat )

sclust : Seeded clustering tool by processing pairwise alignments ( http://compbio.dfci.harvard.edu/tgi/software/ )

screed : Short read sequence utilities ( https://pypi.python.org/pypi/screed http://github.com/ged-lab/screed/ )

scythe : Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa ( https://github.com/vsbuffalo/scythe )

seq_crumbs : Filter, split and trim NGS sequence data ( https://github.com/JoseBlanca/seq_crumbs )

seqclean : Trimpoly and mdust for trimming and validation of ESTs/DNA sequences ( http://compbio.dfci.harvard.edu/tgi/software/ )

seqtools : Display alignments and GFF files, matrix dot plots (blixem, dotter, belvu) ( http://www.sanger.ac.uk/resources/software/seqtools )

sff_dump : Convert Roche SFF files to FASTA file format ( http://genome.imb-jena.de/software/roche454ace2caf )

sga : String Graph OLC Assembler for short reads (overlap-layout-consensus) ( https://github.com/jts/sga )

sgp2 : Find ORFs by comparing two genomic/EST sequences ( http://genome.crg.es/software/sgp2/ )

sickle : Windowed adaptive quality-based trimming tool for FASTQ data ( https://github.com/najoshi/sickle )

signalp : Prediction of signal peptide cleavage sites in amino acid sequences ( http://www.cbs.dtu.dk/services/SignalP/" einfo "Please visit ${HOMEPAGE} and obtain the file )

skewer-bin : Adaptor and MID removal / trimming tool ( http://sourceforge.net/projects/skewer )

smalt : DNA read mapper using k=20 (successor of ssaha2) ( http://www.sanger.ac.uk/resources/software/smalt/ )

smalt-bin : Pairwise sequence alignment mapping DNA reads onto genomic reference ( http://www.sanger.ac.uk/resources/software/smalt/ )

snap : HMM-based prokaryotic and eukaryotic gene prediction tool ( http://korflab.ucdavis.edu/software.html )

snphylo : Pipeline to generate phylogenetic tree from SNP data ( http://chibba.pgml.uga.edu/snphylo )

snpomatic : Stringent short-read aligner supporting filters and various output formats ( https://github.com/magnusmanske/snpomatic )

somatic-sniper : Compare BAM files from normal and tumor samples and report somatic SNPs ( http://gmt.genome.wustl.edu )

spm : Analysis of brain imaging data sequences for Octave or Matlab ( http://www.fil.ion.ucl.ac.uk/spm/ )

sra_sdk : NCBI Sequence Read Archive (SRA) sratoolkit ( http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show%26f=faspftp_runs_v1%26m=downloads%26s=download_sra )

ssaha2-bin : SSAHA2: Sequence Search and Alignment by Hashing Algorithm ( http://www.sanger.ac.uk/resources/software/ssaha2 )

stacks : Analyze restriction enzyme data, draw gen. maps, population genomics ( http://creskolab.uoregon.edu/stacks )

staden : DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin) ( http://sourceforge.net/projects/staden/ )

staden_doc : Documentation files for the staden package ( http://sourceforge.net/projects/staden )

stampy-bin : Map highly divergent short reads to a reference ( http://www.well.ox.ac.uk/project-stampy )

stringtie : Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks ( https://ccb.jhu.edu/software/stringti )

subread : NGS suite for analysis of mapped reads, summary of exon/intron/gene counts ( http://bioinf.wehi.edu.au/featureCounts/ )

swissknife : Perl library of modules to manipulate SwissProt flatfiles ( http://swissknife.sourceforge.net/ )

symap : Synteny Mapping and Analysis Program ( http://www.agcol.arizona.edu/software/symap/ )

tablet : Viewer of next generation sequence assemblies and alignments ( http://bioinf.scri.ac.uk/tablet/ )

tablet-bin : Viewer of next generation sequence assemblies and alignments ( http://ics.hutton.ac.uk/tablet/ )

tagdust : Trim multimers of various primers/adapter from Illumina datasets ( http://genome.gsc.riken.jp/osc/english/dataresource )

tclust : Transitive closure clustering tool with overlap filtering options ( http://compbio.dfci.harvard.edu/tgi/software/ )

tigmint : Correct misassemblies using linked reads from 10x Genomics Chromium ( https://github.com/bcgsc/tigmint )

tigr-foundation-libs : TIGR Foundation for C++ ( http://sourceforge.net/apps/mediawiki/amos/index.php?title=AutoEditor )

tmhmm : Prediction of transmembrane helices in proteins ( http://www.cbs.dtu.dk/services/TMHMM/" einfo "Please visit ${HOMEPAGE} and obtain the file )

trans-abyss : Analyze and combine multiple assemblies from abyss ( http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss )

trf : Tandem Repeats Finder ( http://tandem.bu.edu/trf/trf.html )

trf-bin : Tandem Repeats Finder ( http://tandem.bu.edu/trf/trf.html )

trim_galore : Perl wrapper around Cutadapt and FastQC to adapter and quality trimming ( http://www.bioinformatics.babraham.ac.uk/projects/trim_galore )

trimmomatic : Illumina adapter trimming tool ( http://www.usadellab.org/cms/?page=trimmomatic )

trinityrnaseq : Transcriptome assembler for RNA-seq reads ( http://trinityrnaseq.github.io/ )

trowel : Error corrector for genomic Illumina FASTQ reads ( http://sourceforge.net/projects/trowel-ec )

twinscan : iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure pred. pipeline ( http://mblab.wustl.edu/software/twinscan )

ugene : A free open-source cross-platform bioinformatics software ( http://ugene.unipro.ru )

vague-bin : GUI for Velvet de novo assembler ( http://www.vicbioinformatics.com/software.vague.shtml )

vcflib : VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++) ( https://github.com/vcflib/vcflib )

vcftools : Tools for working with VCF (Variant Call Format) files ( http://vcftools.sourceforge.net/ )

velvetk : Estimate the best k-mer size to use for your Velvet de novo assembly ( http://www.vicbioinformatics.com/software.velvetk.shtml )

verifyBamID : Verify sample identity/mix and genotype concordance ( http://genome.sph.umich.edu/wiki/VerifyBamID )

vt : A tool set for short variant discovery in genetic sequence data ( https://github.com/atks/v )

wcd : EST sequence clustering: d2 function, edit distance, common word heuristics ( http://code.google.com/p/wcdest/ )

weblogo : generate consensus sequence logo figures ( http://weblogo.berkeley.edu/ )

wgs-assembler : De novo whole-genome shotgun DNA sequence OLC assembler ( http://sourceforge.net/projects/wgs-assembler/ )

wgs_tools : Scripts for ncbi-tools++ and SRA postprocessing using taxonomy ( ftp://ftp.ncbi.nih.gov/blast/WGS_TOOL )

wise : Genewise, promoterwise: align protein HMMs to DNA for CDS predictions ( http://www.ebi.ac.uk/~birney/wise2 )

yaha : DNA mapper for single-end reads to detect structural variants (SV) ( https://github.com/GregoryFaust/yaha )

zmap : A desktop genome browser using GFF inputs ( http://www.sanger.ac.uk/science/tools/zmap )

zmsort : Merge-sort utility for compressed alignment files, with multi-file output ( http://compbio.dfci.harvard.edu/tgi/software/ )

Add an ebuild in portage :

The ebuild is now in the portage tree.

You can also use layman : emerge layman then layman -a science

For Paludis use this rsync : rsync://gentoo.zugaina.org/science-portage

If you have a problem : ycarus(-at-)zugaina.org