Gentoo Project

Biology Project

Outdated Packages

• sci-biology/abyss

  Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
• sci-biology/augustus

  Eukaryotic gene predictor
• sci-biology/bedtools

  Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats
• sci-biology/bioperl

  Perl tools for bioinformatics - Core modules
• sci-biology/bioperl-network

  Perl tools for bioinformatics - Analysis of protein-protein interaction networks
• sci-biology/bioperl-run

  Perl wrapper modules for key bioinformatics applications
• sci-biology/blat

  The BLAST-Like Alignment Tool, a fast genomic sequence aligner
• sci-biology/cd-hit

  Clustering Database at High Identity with Tolerance
• sci-biology/clustalw-mpi

  An MPI implemention of the ClustalW general purpose multiple alignment algorithm
• sci-biology/exonerate

  Generic tool for pairwise sequence comparison
• sci-biology/fasta

  FASTA is a DNA and Protein sequence alignment software package
• sci-biology/gmap

  A Genomic Mapping and Alignment Program for mRNA and EST Sequences
• sci-biology/infernal

  Inference of RNA alignments
• sci-biology/kalign

  Global and progressive multiple sequence alignment
• sci-biology/kallisto

  Near-optimal RNA-Seq quantification
• sci-biology/libgtextutils

  Gordon Text utils Library
• sci-biology/mafft

  Multiple sequence alignments using a variety of algorithms
• sci-biology/mothur

  A suite of algorithms for ecological bioinformatics
• sci-biology/mrbayes

  Bayesian Inference of Phylogeny
• sci-biology/muscle

  Multiple sequence comparison by log-expectation
• sci-biology/paml

  Phylogenetic Analysis by Maximum Likelihood
• sci-biology/raxml

  Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
• sci-biology/seaview

  A graphical multiple sequence alignment editor
• sci-biology/seqan

  C++ Sequence Analysis Library
• sci-biology/sim4

  A program to align cDNA and genomic DNA
• sci-biology/STAR

  STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays
• sci-biology/stride

  Protein secondary structure assignment from atomic coordinates
• sci-biology/trf

  Tandem Repeats Finder
• sci-biology/trnascan-se

  tRNA detection in large-scale genome sequences
• sci-biology/wise

  Intelligent algorithms for DNA searches
• sci-visualization/circos

  Circular layout visualization of genomic and other data