Gentoo Project

Biology Project

acct-group

• acct-group/foldingathome

  A group for sci-biology/foldingathome

acct-user

• acct-user/foldingathome

  A user for sci-biology/foldingathome

dev-libs

• dev-libs/igraph

  Creating and manipulating undirected and directed graphs

dev-perl

• dev-perl/Bio-DB-HTS

  Perl bindings for sci-libs/htslib
• dev-perl/librg-utils-perl

  Parsers and format conversion utilities used by (e.g.) profphd

dev-python

• dev-python/intervaltree

  Editable interval tree data structure for Python 2 and 3

sci-biology

• sci-biology/aaindex

  Amino acid indices and similarity matrices
• sci-biology/abyss

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

  Protein multiple-alignment-based sequence annealing
• sci-biology/augustus

  Eukaryotic gene predictor
• sci-biology/bamtools

  A programmer's API and an end-user's toolkit for handling BAM files
• sci-biology/bcftools

  Utilities for variant calling and manipulating VCF and BCF files
• sci-biology/bedtools

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

  Blat-like Fast Accurate Search Tool
• sci-biology/biogrep

  Multithreaded tool for matching large sets of patterns against biosequence DBs
• sci-biology/bioperl

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

  Perl tools for bioinformatics - Perl API that accesses the BioSQL schema
• 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/biopython

  Python modules for computational molecular biology
• sci-biology/biosql

  A generic bioinformatics relational database model
• sci-biology/blat

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

  Popular short read aligner for Next-generation sequencing data
• sci-biology/bwa

  Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner
• sci-biology/cd-hit

  Clustering Database at High Identity with Tolerance
• sci-biology/clustal-omega

  Scalable multiple alignment of protein sequences
• sci-biology/clustalw

  General purpose multiple alignment program for DNA and proteins
• sci-biology/clustalw-mpi

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

  Graphical interface for the ClustalW multiple alignment program
• sci-biology/cutg

  Codon usage tables calculated from GenBank
• sci-biology/dialign2

  Multiple sequence alignment
• sci-biology/dialign-tx

  Greedy and progressive approaches for segment-based multiple sequence alignment
• sci-biology/elph

  Estimated Locations of Pattern Hits - Motif finder program
• sci-biology/embassy

  A meta-package for installing all EMBASSY packages (EMBOSS add-ons)
• sci-biology/embassy-cbstools

  EMBOSS integrated version of Applications from the CBS group
• sci-biology/embassy-clustalomega

  EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment
• sci-biology/embassy-domainatrix

  EMBOSS integrated version of Protein domain analysis add-on package
• sci-biology/embassy-domalign

  EMBOSS integrated version of Protein domain alignment add-on package
• sci-biology/embassy-domsearch

  EMBOSS integrated version of Protein domain search add-on package
• sci-biology/embassy-emnu

  EMBOSS integrated version of Simple menu of EMBOSS applications
• sci-biology/embassy-esim4

  EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA
• sci-biology/embassy-hmmer

  EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs
• sci-biology/embassy-iprscan

  EMBOSS integrated version of InterProScan motif detection add-on package
• sci-biology/embassy-mse

  EMBOSS integrated version of MSE - Multiple Sequence Screen Editor
• sci-biology/embassy-phylipnew

  EMBOSS integrated version of The Phylogeny Inference Package
• sci-biology/embassy-signature

  EMBOSS integrated version of Protein signature add-on package
• sci-biology/embassy-structure

  EMBOSS integrated version of Protein structure add-on package
• sci-biology/embassy-topo

  EMBOSS integrated version of Transmembrane protein display
• sci-biology/embassy-vienna

  EMBOSS integrated version of Vienna RNA package - RNA folding
• sci-biology/emboss

  The European Molecular Biology Open Software Suite - A sequence analysis package
• sci-biology/eugene

  Prokaryotic and Eukaryotic gene predictor
• sci-biology/exonerate

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

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

  Fast inference of approximately-maximum-likelihood phylogenetic trees
• sci-biology/finchtv

  Graphical viewer for chromatogram files
• sci-biology/foldingathome

  Folding@Home is a distributed computing project for protein folding
• sci-biology/glimmer

  An HMM-based microbial gene finding system from TIGR
• sci-biology/glimmerhmm

  A eukaryotic gene finding system from TIGR
• sci-biology/gmap

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

  Sequence analysis using profile hidden Markov models
• sci-biology/HTSeq

  Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files
• sci-biology/iedera

  Subset seed design tool for DNA sequence alignment
• sci-biology/infernal

  Inference of RNA alignments
• sci-biology/iqpnni

  Important Quartet Puzzling and NNI Operation
• sci-biology/kalign

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

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

  The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
• sci-biology/libgtextutils

  Gordon Text utils Library
• sci-biology/mafft

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

  Mapping and Assembly with Qualities, mapping NGS reads to reference genomes
• sci-biology/maqview

  GUI for sci-biology/maq, a short read mapping assembler
• sci-biology/mcl

  A Markov Cluster Algorithm implementation
• sci-biology/mosaik

  A reference-guided aligner for next-generation sequencing technologies
• sci-biology/mothur

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

  Bayesian Inference of Phylogeny
• sci-biology/mummer

  A rapid whole genome aligner
• sci-biology/muscle

  Multiple sequence comparison by log-expectation
• sci-biology/newick-utils

  Tools for processing phylogenetic trees
• sci-biology/pals

  Pairwise Aligner for Long Sequences
• sci-biology/paml

  Phylogenetic Analysis by Maximum Likelihood
• sci-biology/phylip

  The PHYLogeny Inference Package
• sci-biology/phyml

  Estimation of large phylogenies by maximum likelihood
• sci-biology/piler

  Analysis of repetitive DNA found in genome sequences
• sci-biology/pilercr

  Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
• sci-biology/plink

  Whole genome association analysis toolset
• sci-biology/poa

  Fast multiple sequence alignments using partial-order graphs
• sci-biology/prank

  Probabilistic Alignment Kit
• sci-biology/primer3

  Primer Design for PCR reactions
• sci-biology/prints

  A protein motif fingerprint database
• sci-biology/probcons

  Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
• sci-biology/prodigal

  Prokaryotic Dynamic Programming Genefinding Algorithm
• sci-biology/profphd

  Secondary structure and solvent accessibility predictor
• sci-biology/prosite

  A protein families and domains database
• sci-biology/pysam

  Python interface for the SAM/BAM sequence alignment and mapping format
• sci-biology/qrna

  Prototype ncRNA genefinder
• sci-biology/raxml

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

  A restriction enzyme database
• sci-biology/recon

  Automated de novo identification of repeat families from genomic sequences
• sci-biology/rnaview

  Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
• sci-biology/samtools

  Utilities for analysing and manipulating the SAM/BAM alignment formats
• sci-biology/seaview

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

  C++ Sequence Analysis Library
• sci-biology/sibsim4

  A rewrite and improvement upon sim4, a DNA-mRNA aligner
• 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/t-coffee

  A multiple sequence alignment package
• sci-biology/tree-puzzle

  Maximum likelihood analysis for nucleotide, amino acid, and two-state data
• sci-biology/treeviewx

  A phylogenetic tree viewer
• sci-biology/trf

  Tandem Repeats Finder
• sci-biology/trnascan-se

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

  Fast, accurate chimera detection
• sci-biology/ucsc-genome-browser

  The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
• sci-biology/unafold

  Unified Nucleic Acid Folding and hybridization package
• sci-biology/update-blastdb

  update_blastdb.pl for local blast db maintainance
• sci-biology/vcftools

  Tools for working with VCF (Variant Call Format) files
• sci-biology/velvet

  A sequence assembler for very short reads
• sci-biology/wise

  Intelligent algorithms for DNA searches
• sci-biology/yass

  Genomic similarity search with multiple transition constrained spaced seeds

sci-libs

• sci-libs/dcmtk

  The DICOM Toolkit
• sci-libs/htslib

  C library for high-throughput sequencing data formats
• sci-libs/libmuscle

  Library for sci-biology/mauve
• sci-libs/profnet

  Neural network architecture for profacc
• sci-libs/profphd-utils

  Additional utils for profphd

sci-visualization

• sci-visualization/circos

  Circular layout visualization of genomic and other data