ApE : A Plasmid Editor ( http://www.biology.utah.edu/jorgensen/wayned/ape/ )
GBrowse : Generic Model Organism Database Project - The Generic Genome Browser ( http://gmod.org/wiki/GBrowse )
aaindex : Amino acid indices and similarity matrices ( http://www.genome.ad.jp/aaindex )
abyss : Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler ( http://www.bcgsc.ca/platform/bioinfo/software/abyss/ )
allpathslg : De novo assembly of whole-genome shotgun microreads ( http://www.broadinstitute.org/science/programs/genome-biology/crd )
amap : Protein multiple-alignment-based sequence annealing ( http://bio.math.berkeley.edu/amap/ )
amos : A Modular, Open-Source whole genome assembler ( http://amos.sourceforge.net/ )
arb : Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis ( http://www.arb-home.de/ )
ariadne : Protein sequences and profiles comparison ( http://www.well.ox.ac.uk/ariadne/ )
augustus : Eukaryotic gene predictor ( http://augustus.gobics.de/ )
bamtools : A programmer's API and an end-user's toolkit for handling BAM files ( https://github.com/pezmaster31/bamtools )
beast-mcmc : Bayesian MCMC of Evolution and Phylogenetics using Molecular Sequences ( https://github.com/beast-dev/beast-mcmc )
bedtools : Tools for manipulation and analysis of BED, GFF/GTF, VCF, and SAM/BAM file formats ( https://github.com/arq5x/bedtools2 )
bfast : Blat-like Fast Accurate Search Tool ( https://sourceforge.net/projects/bfast/ )
biogrep : Multithreading application for matching large sets of patternsagainst biosequence dbs ( http://web.mit.edu/bamel/biogrep.shtml )
biojava : A Java framework for processing biological data ( http://biojava.org )
bioperl : Perl tools for bioinformatics - Core modules ( http://www.bioperl.org/ )
bioperl-db : Perl tools for bioinformatics - Perl API that accesses the BioSQL schema ( http://www.bioperl.org/ )
bioperl-network : Perl tools for bioinformatics - Analysis of protein-protein interaction networks ( http://www.bioperl.org/ )
bioperl-run : Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications ( http://www.bioperl.org/ )
biopython : Python modules for computational molecular biology ( http://www.biopython.org/ https://pypi.python.org/pypi/biopython/ )
bioruby : An integrated environment for bioinformatics using the Ruby language ( http://www.bioruby.org/ )
biosql : A generic bioinformatics relational database model ( http://www.biosql.org/ )
blat : The BLAST-Like Alignment Tool, a fast genomic sequence aligner ( http://www.cse.ucsc.edu/~kent/ )
blossoc : A linkage disequilibrium association mapping tool ( http://www.daimi.au.dk/~mailund/Blossoc/ )
bowtie : An ultrafast memory-efficient short read aligner ( http://bowtie-bio.sourceforge.net/ )
bwa : Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner ( http://bio-bwa.sourceforge.net/ )
cd-hit : Clustering Database at High Identity with Tolerance ( http://weizhong-lab.ucsd.edu/cd-hit/ )
clustal-omega : Scalable multiple alignment of protein sequences ( http://www.clustal.org/omega/ )
clustalw : General purpose multiple alignment program for DNA and proteins ( http://www.clustal.org/ )
clustalw-mpi : A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm ( http://www.bii.a-star.edu.sg/achievements/applications/clustalw/index.php )
clustalx : Graphical interface for the ClustalW multiple alignment program ( http://www.ebi.ac.uk/tools/clustalw2/ )
consed : A genome sequence finishing program ( http://bozeman.mbt.washington.edu/consed/consed.html" einfo "Please visit ${HOMEPAGE} and obtain the file )
cufflinks : Transcript assembly, differential expression, and differential regulation for RNA-Seq ( http://cufflinks.cbcb.umd.edu/ )
cutg : Codon usage tables calculated from GenBank ( http://www.kazusa.or.jp/codon/ )
dialign-tx : Greedy and progressive approaches for segment-based multiple sequence alignment ( http://dialign-tx.gobics.de/ )
dialign2 : Multiple sequence alignment ( http://bibiserv.techfak.uni-bielefeld.de/dialign )
diya : Do It Yourself Annotation, a collection of tools and libraries for sequence assembly and annotation ( http://gmod.org/wiki/Diya )
elph : Estimated Locations of Pattern Hits - Motif finder program ( http://cbcb.umd.edu/software/ELPH/ )
embassy : A meta-package for installing all EMBASSY packages (EMBOSS add-ons) ( http://emboss.sourceforge.net/embassy/ )
embassy-cbstools : Applications from the CBS group ( )
embassy-clustalomega : Clustal Omega - Scalable multiple protein sequences alignment ( )
embassy-domainatrix : Protein domain analysis add-on package ( )
embassy-domalign : Protein domain alignment add-on package ( )
embassy-domsearch : Protein domain search add-on package ( )
embassy-emnu : Simple menu of EMBOSS applications ( )
embassy-esim4 : sim4 - Alignment of cDNA and genomic DNA ( )
embassy-hmmer : Wrappers for HMMER - Biological sequence analysis with profile HMMs ( )
embassy-iprscan : InterProScan motif detection add-on package ( )
embassy-meme : Wrappers for MEME - Multiple Em for Motif Elicitation ( )
embassy-mse : MSE - Multiple Sequence Screen Editor ( )
embassy-phylipnew : The Phylogeny Inference Package ( )
embassy-signature : Protein signature add-on package ( )
embassy-structure : Protein structure add-on package ( )
embassy-topo : Transmembrane protein display ( )
embassy-vienna : Vienna RNA package - RNA folding ( )
emboss : The European Molecular Biology Open Software Suite - A sequence analysis package ( )
eugene : Eukaryotic gene predictor ( http://www.inra.fr/mia/T/EuGene/ )
exonerate : Generic tool for pairwise sequence comparison ( http://www.ebi.ac.uk/~guy/exonerate/ )
express : Streaming RNA-Seq Analysis ( http://bio.math.berkeley.edu/eXpress/ )
fasta : FASTA is a DNA and Protein sequence alignment software package ( http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml )
fasttree : Fast inference of approximately-maximum-likelihood phylogenetic trees ( http://www.microbesonline.org/fasttree/ )
finchtv : Graphical viewer for chromatogram files ( http://www.geospiza.com/finchtv/ )
foldingathome : Folding@Home is a distributed computing project for protein folding ( http://folding.stanford.edu/FAQ-SMP.html )
gatk : The Genome Analysis Toolkit ( http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit )
gibbs : Identify motifs, conserved regions, in DNA or protein sequences ( http://bayesweb.wadsworth.org/gibbs/gibbs.html )
glimmer : An HMM-based microbial gene finding system from TIGR ( http://ccb.jhu.edu/software/glimmer )
glimmerhmm : A eukaryotic gene finding system from TIGR ( http://www.cbcb.umd.edu/software/GlimmerHMM/ )
gmap : A Genomic Mapping and Alignment Program for mRNA and EST Sequences ( http://research-pub.gene.com/gmap/ )
goby : A DNA sequencing data management framework ( http://campagnelab.org/software/goby/ )
goby-cpp : A DNA sequencing data management framework - C/C++ API ( http://campagnelab.org/software/goby/ )
hmmer : Sequence analysis using profile hidden Markov models ( http://hmmer.janelia.org/ )
iedera : A subset seed design tool for DNA sequence alignment ( http://bioinfo.lifl.fr/yass/iedera.php )
infernal : Inference of RNA alignments ( http://infernal.janelia.org/ )
iqpnni : Important Quartet Puzzling and NNI Operation ( http://www.cibiv.at/software/iqpnni/ )
kalign : Global and progressive multiple sequence alignment ( http://msa.cgb.ki.se/ )
lagan : LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA ( http://lagan.stanford.edu/lagan_web/index.shtml )
last : Genome-scale comparison of biological sequences ( http://last.cbrc.jp/ )
mafft : Multiple sequence alignments using a variety of algorithms ( http://mafft.cbrc.jp/alignment/software/index.html )
mammoth : MAtching Molecular Models Obtained from THeory ( http://ub.cbm.uam.es/software.php" einfo "${HOMEPAGE} )
maq : Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences ( http://maq.sourceforge.net/ )
maqview : GUI for sci-biology/maq, a short read mapping assembler ( http://maq.sourceforge.net/ )
mauve : Multiple genome alignment with large-scale evolutionary events (GUI component) ( http://gel.ahabs.wisc.edu/mauve/ )
mauvealigner : Multiple genome alignment with large-scale evolutionary events (aligner component) ( http://gel.ahabs.wisc.edu/mauve/ )
mcl : A Markov Cluster Algorithm implementation ( http://micans.org/mcl/ )
meme : The MEME/MAST system - Motif discovery and search ( http://meme.sdsc.edu/meme )
mira : Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina ( http://www.chevreux.org/projects_mira.html )
mosaik : A reference-guided aligner for next-generation sequencing technologies ( https://code.google.com/p/mosaik-aligner/ )
mothur : A suite of algorithms for ecological bioinformatics ( http://www.mothur.org/ )
mrbayes : Bayesian Inference of Phylogeny ( http://mrbayes.csit.fsu.edu/ )
mummer : A rapid whole genome aligner ( http://mummer.sourceforge.net/ )
muscle : Multiple sequence comparison by log-expectation ( http://www.drive5.com/muscle/ )
ncbi-tools : Development toolkit and applications for computational biology, including NCBI BLAST ( http://www.ncbi.nlm.nih.gov/ )
newick-utils : Tools for processing phylogenetic trees (re-root, subtrees, trimming, pruning, condensing, drawing) ( http://cegg.unige.ch/newick_utils )
njplot : A phylogenetic tree drawing program which supports tree rooting ( http://pbil.univ-lyon1.fr/software/njplot.html )
paml : Phylogenetic Analysis by Maximum Likelihood ( http://abacus.gene.ucl.ac.uk/software/paml.html )
phrap : Shotgun assembly and alignment utilities ( http://www.phrap.org/ )
phred : A base caller for Sanger DNA sequencing ( http://phrap.org/phredphrapconsed.html" elog "Please visit ${HOMEPAGE} and obtain the file )
phylip : The PHYLogeny Inference Package ( http://evolution.genetics.washington.edu/phylip.html )
phyml : Estimation of large phylogenies by maximum likelihood ( http://atgc.lirmm.fr/phyml/ )
picard : Java-based command-line utilities that manipulate SAM files ( http://picard.sourceforge.net/ )
piler : Analysis of repetitive DNA found in genome sequences ( http://www.drive5.com/piler/ )
pilercr : Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) ( http://www.drive5.com/pilercr/ )
plink : Whole genome association analysis toolset ( http://pngu.mgh.harvard.edu/~purcell/plink/ )
poa : Fast multiple sequence alignments using partial-order graphs ( http://bioinfo.mbi.ucla.edu/poa/ )
prank : Probabilistic Alignment Kit ( http://wasabiapp.org/software/prank/ )
primer3 : Primer Design for PCR reactions ( http://primer3.sourceforge.net/ )
prints : A protein motif fingerprint database ( http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ )
probcons : Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences ( http://probcons.stanford.edu/ )
prodigal : Prokaryotic Dynamic Programming Genefinding Algorithm ( http://prodigal.ornl.gov/ https://code.google.com/p/prodigal/ )
profphd : Secondary structure and solvent accessibility predictor ( https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction )
prosite : A protein families and domains database ( http://ca.expasy.org/prosite )
psipred : Protein Secondary Structure Prediction ( http://bioinf.cs.ucl.ac.uk/psipred/ )
pysam : Python interface for the SAM/BAM sequence alignment and mapping format ( https://code.google.com/p/pysam https://pypi.python.org/pypi/pysam )
qrna : Prototype ncRNA genefinder ( http://selab.janelia.org/software.html )
raxml : Sequential, Parallel and Distributed Inference of Large Phylogenetic Trees ( http://wwwkramer.in.tum.de/exelixis/software.html )
readseq : Reads and writes nucleic/protein sequences in various formats ( http://iubio.bio.indiana.edu/soft/molbio/readseq/ )
recon : Automated de novo identification of repeat families from genomic sequences ( http://selab.janelia.org/recon.html http://www.repeatmasker.org/RepeatModeler.html )
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/ )
rmblast : RepeatMasker compatible version of NCBI BLAST+ ( http://www.repeatmasker.org/RMBlast.html )
rnaview : Generates 2D displays of RNA/DNA secondary structures with tertiary interactions ( http://ndbserver.rutgers.edu/services/download/index.html )
samtools : Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments ( http://www.htslib.org/ )
seaview : A graphical multiple sequence alignment editor ( http://pbil.univ-lyon1.fr/software/seaview.html )
seqan : C++ Sequence Analysis Library ( http://www.seqan.de/ )
shrimp : SHort Read Mapping Package ( http://compbio.cs.toronto.edu/shrimp/ )
sibsim4 : A rewrite and improvement upon sim4, a DNA-mRNA aligner ( http://sibsim4.sourceforge.net/ )
sim4 : A program to align cDNA and genomic DNA ( http://globin.cse.psu.edu/html/docs/sim4.html )
snpfile : A library and API for manipulating large SNP datasets ( http://www.birc.au.dk/~mailund/SNPFile/ )
stride : Protein secondary structure assignment from atomic coordinates ( http://webclu.bio.wzw.tum.de/stride/ )
t-coffee : A multiple sequence alignment package ( http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html )
tophat : A fast splice junction mapper for RNA-Seq reads ( http://tophat.cbcb.umd.edu/ )
transfac : A database of eucaryotic transcription factors ( http://www.gene-regulation.com/pub/databases.html )
tree-puzzle : Maximum likelihood analysis for nucleotide, amino acid, and two-state data ( http://www.tree-puzzle.de )
treeviewx : A phylogenetic tree viewer ( http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ )
trnascan-se : tRNA detection in large-scale genome sequences ( http://lowelab.ucsc.edu/tRNAscan-SE/ )
uchime : Fast, accurate chimera detection ( http://www.drive5.com/uchime/ )
ucsc-genome-browser : The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath ( http://genome.ucsc.edu/ )
unafold : Unified Nucleic Acid Folding and hybridization package ( http://mfold.rna.albany.edu/ )
update-blastdb : update_blastdb.pl for local blast db maintainance ( http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit )
vaal : A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms ( http://www.broadinstitute.org/science/programs/genome-biology/crd/ )
vcftools : Tools for working with VCF (Variant Call Format) files ( http://vcftools.sourceforge.net/ )
velvet : A sequence assembler for very short reads ( http://www.ebi.ac.uk/~zerbino/velvet/ )
vienna-rna : RNA secondary structure prediction and comparison ( http://www.tbi.univie.ac.at/~ivo/RNA/ )
wgs-assembler : A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG ( http://sourceforge.net/projects/wgs-assembler/ )
wise : Intelligent algorithms for DNA searches ( http://www.ebi.ac.uk/Wise2/ )
yass : Genomic similarity search with multiple transition constrained spaced seeds ( http://bioinfo.lifl.fr/yass/ )
Add an ebuild in portage :
The ebuild is now in the portage tree.
You can also use layman : emerge layman then layman -a gentoo
For Paludis use this rsync : rsync://gentoo.zugaina.org/gentoo-portage
If you have a problem : ycarus(-at-)zugaina.org