Ycarus Gentoo ebuild

science

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sci-biology

ABI-connectivity-data : Connectivity data from the Allen Mouse Brain data portal ( https://github.com/IBT-FMI/ABI-connectivity-data_generator )

ABI-expression-data : Gene expression data form the Allen Mouse Brain data portal ( https://github.com/IBT-FMI/ABI-expression-data_generator )

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 )

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

BRAKER : Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS ( https://github.com/Gaius-Augustus/BRAKE )

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

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

CAT : Codon usage bias (composition) and its statistical significance ( HOMEPAGE=" )

FLASH : Paired-end mates merge from fragments ( https://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) ( https://github.com/The-Sequence-Ontology/GAL )

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

KING : Check family relationship and infer population structure ( https://kingrelatedness.com )

KaKs_Calculator : Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates ( HOMEPAGE=" )

LINKS : Scaffold genome assemblies by Chromium/PacBio/Nanopore reads ( https://github.com/bcgsc/LINKS )

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

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

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

MolBioLib : C++11 framework for bioinformatics tasks ( https://sourceforge.net/projects/molbiolib )

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

NGSEPcore : NGSEP (CNV and indel discovery) ( https://sourceforge.net/p/ngsep/wiki/Hom )

NGSEPcore-bin : NGSEP (CNV and indel discovery) ( https://sourceforge.net/p/ngsep/wiki/Hom )

OBO-Edit : Java-based editor optimized for the OBO biological ontology file format ( http://www.oboedit.org/" # no https, invalid certificat )

ONTO-PERL : Manipulates OBO- and OWL-formatted ontologies (like the Gene Ontology) ( https://metacpan.org/release/ONTO-PERL )

ParaAT : Create multiple protein-coding DNA alignments and back-Translation ( http://cbb.big.ac.cn/softwar )

RAILS : Cobbler and RAILS scaffolding tools acting on SAM streams ( https://github.com/bcgsc/RAILS )

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

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 ( https://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 )

SnpEff : SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF ( https://pcingola.github.io/SnpEff/ )

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

TransDecoder : Extract ORF/CDS regions from FASTA sequences ( https://github.com/TransDecoder/TransDecoder/wiki )

Trinotate : Annotation and analysis pipeline for de novo assembled transcriptomes ( https://github.com/Trinotate/Trinotate.github.io/wiki )

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 ( https://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 )

abyss : Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler ( http://www.bcgsc.ca/platform/bioinfo/software/abyss/ )

act-bin : DNA contig sequence comparison tool supplementing Artemis ( https://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 )

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

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

arachne : Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig) ( https://genome.cshlp.org/content/12/1/177.abstract )

arcs : Scaffold genome sequence assemblies by Chromium/PacBio/Naopore reads ( https://github.com/bcgsc/arcs )

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

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

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

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

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

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

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

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

behaviopy : Neuroimaging tools for Python ( https://github.com/TheChymera/behaviopy )

biobambam2 : Tools for bam file processing (using libmaus2) ( https://gitlab.com/german.tischler/biobambam )

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

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

bowtie : Popular short read aligner for Next-generation sequencing data ( http://bowtie-bio.sourceforge.net/bowtie2/ )

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/ )

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

bruker2nifti : Medical image converter, from raw Bruker ParaVision to NIfTI ( https://github.com/SebastianoF/bruker2nifti )

btl_bloomfilter : BTL C/C common bloom filters ( https://github.com/bcgsc/btl_bloomfilter )

bx-python : Library for rapid implementation of genome scale analyses ( https://github.com/bxlab/bx-python )

caftools : Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/ )

canu : Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences ( https://canu.readthedocs.io/en/latest )

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

cdbfasta : FASTA record indexing/retrievieng utility ( https://github.com/gpertea/cdbfasta )

chiron : A deep neural network basecaller for nanopore sequencing ( https://github.com/haotianteng/chiro )

cluster : Hierarchical, k-means, k-medians clustering for expression/microarray analysis ( http://bonsai.hgc.jp/~mdehoon/software/cluste )

clview : clview is an assembly .ace file viewer from TIGR Gene Indices project tools ( https://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 ( https://faculty.washington.edu/browning/conform-gt.html )

conrad : Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor ( https://sourceforge.net/projects/conradcrf )

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" # no http )

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 ( https://www.sanger.ac.uk/tool/crossgenome/ )

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

dargcc_bidsdata : BIDS data selection of wildtype animals from DARGCC article ( https://academic.oup.com/cercor/article/28/7/2495/4975475 )

dcm2niix : DICOM to NIfTI converter ( https://github.com/rordenlab/dcm2niix )

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/deeptools/deepTools )

deeptools-intervals : Constructing interval trees with associated exon/annotation information ( https://github.com/deeptools/deeptools_intervals )

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 ( https://github.com/nipy/dipy )

drlfom_bidsdata : BIDS data files released with the DRLFOM publication ( http://www.aic-fmi.ethz.ch/ )

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

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://rna.igmors.u-psud.fr )

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

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 ( https://directory.fsf.org/wiki/FastDNAml )

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

ffindex : Simple index/database for huge amounts of small files ( https://github.com/ahcm/ffindex )

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 ( https://www.fmrib.ox.ac.uk/fsl )

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

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

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://gusevlab.org/projects/germline )

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 )

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

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

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 ( https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi )

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

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=" )

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

imagej : Image Processing and Analysis in Java ( https://imagej.nih.gov/ij/ )

irsabi_bidsdata : BIDS data files released with the IRSABI publication ( http://www.aic-fmi.ethz.ch/ )

jannovar-bin : Exome annotation tool (upstream jar binaries) ( https://jannovar.readthedocs.io/en/master/ )

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 ( https://www.cbcb.umd.edu/software/jigsaw )

jtreeview : Viewer for Microarray Data in PCL or CDT formats ( http://jtreeview.sourceforge.net/" # no http )

jtreeview-bin : Viewer for Microarray Data in PCL or CDT formats ( http://jtreeview.sourceforge.net/" # no http )

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/dib-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 ( https://ccb.jhu.edu/software/kraken2/ )

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/ )

lemur-brain-atlas : MRI Brain Template and Atlas of the Mouse Lemur ( https://www.nitrc.org/projects/mouselemuratlas )

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

libblasr : Library for blasr ( http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR )

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

longstitch : Scaffold genome assemblies by Chromium/PacBio/Nanopore reads ( https://github.com/bcgsc/LongStitch )

lucy : DNA sequence quality and vector trimming tool ( http://lucy.sourceforge.net/" # no http )

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

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

manatee-igs : IGS-modified version of the genome annotation tool using Chado database schema ( http://manatee.sourceforge.net/igs" # no http )

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

mappy : Minimap2 python binding ( https://github.com/haotianteng/chiron )

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

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

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

minimap2 : splice-aware sequence aligner ( https://github.com/lh3/minimap2 )

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

miranda : An algorithm for finding genomic targets for microRNAs ( https://www.mskcc.org/research/ski/programs/computational-biology )

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

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

mreps : Identification of serial/tandem repeats in DNA sequences ( https://mreps.univ-mlv.fr/ )

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

mrsfast : Micro Read Fast Alignment Search Tool ( https://sfu-compbio.github.io/mrsfast/ )

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+ ( https://ncbi.github.io/cxx-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+ ( https://ncbi.github.io/cxx-toolkit/ )

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

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

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

nrcl : Containment clustering and layout utility for processing pairwise alignments ( https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/ )

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

nwalign3 : Needleman-Wunsch global sequence alignment in python3 ( https://github.com/briney/nwalign3 )

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 )

open-ephys-gui : Processing, recording, and visualizing multichannel ephys data ( https://open-ephys.org/gui/ )

opfvta_bidsdata : BIDS data files released with the OPFVTA publication ( http://www.aic-fmi.ethz.ch/ )

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

parafly : Parallel cmd processing utility ( https://github.com/ParaFly/ParaFly )

pbbam : PacBio modified BAM file format ( https://pbbam.readthedocs.io/en/latest/index.html )

pbcopper : Core C++ library for data structures, algorithms, and utilities ( https://github.com/PacificBiosciences/pbcopper )

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/ )

phusion2 : Whole genome shotgun assembler using phrap (for Sanger-based reads) ( https://sourceforge.net/projects/phusion2 )

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

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

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

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

primerD : Design degenerate primers ( https://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 ( https://vicbioinformatics.com/software.prokka.shtml )

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

psx : parallel multi-FASTA file processing tool from TIGR Gene Indices project tools ( https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/ )

pufferfish : Index for the colored, compacted, de Bruijn graph ( https://github.com/COMBINE-lab/pufferfish )

pybedtools : Use BED and GFF files from python using BEDtools ( https://daler.github.io/pybedtools )

pyfaidx : Efficient pythonic random access to fasta subsequences ( https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx )

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

quast : Compare quality of multiple genome assemblies to each other ( http://bioinf.spbau.ru/QUAST" # no http )

quicktree : Rapid reconstruction of phylogenies by the Neighbor-Joining method ( https://github.com/khowe/quicktree/ )

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

rat-brain-templates : A collection of rat brain templates in NIfTI format ( https://gitlab.com/FOS-FMI/rat-brain-templates_generator )

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

roche454ace2caf : ace to gap4 converter ( https://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 )

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 ( https://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 ( https://lomereiter.github.io/sambamba/ )

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

samri_bidsdata : BIDS-formatted example mouse brain data for SAMRI ( https://github.com/IBT-FMI/SAMRI )

samri_bindata : ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI ( https://github.com/IBT-FMI/SAMRI )

samstat : Statistics of BAM/SAM files ( http://samstat.sourceforge.net" # no http )

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

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

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

seqtk : Manipulate FASTA and FASTQ files ( https://github.com/lh3/seqtk )

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 )

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 ( https://sourceforge.net/projects/skewer )

smalt : DNA read mapper using k=20 (successor of ssaha2) ( https://sourceforge.net/projects/smalt/ )

smalt-bin : Pairwise sequence alignment mapping DNA reads onto genomic reference ( https://sourceforge.net/projects/smalt/ )

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

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

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

sra_sdk : NCBI Sequence Read Archive (SRA) sratoolkit ( https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools )

ssaha2-bin : SSAHA2: Sequence Search and Alignment by Hashing Algorithm ( https://www.sanger.ac.uk/tool/ssaha2-0/ )

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) ( https://sourceforge.net/projects/staden/ )

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

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/" # no http )

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/ https://github.com/csoderlund/SyMAP )

tabixpp : C++ wrapper to tabix indexer ( https://github.com/ekg/tabixpp )

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

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

tigr-foundation-libs : TIGR Foundation for C++ ( https://sourceforge.net/projects/amos/ )

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 ( https://www.bcgsc.ca/resources/software/trans-abyss )

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 ( https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ https://github.com/FelixKrueger/TrimGalore )

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

trinityrnaseq : Transcriptome assembler for RNA-seq reads ( https://github.com/Trinotate/Trinotate.github.io/wiki )

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

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

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

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

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 ( https://shaze.github.io/wcdest/ )

weblogo : generate consensus sequence logo figures ( http://weblogo.threeplusone.com/ )

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

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 ( https://www.sanger.ac.uk/science/tools/zmap )

zmsort : Merge-sort utility for compressed alignment files, with multi-file output ( https://web.archive.org/web/20140726030702/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