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Browse sci-biology in overlay gentoo

aaindex
Amino acid indices and similarity matrices
abyss
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
amap
augustus
Eukaryotic gene predictor
bamtools
bcftools
bedtools
bfast
Blat-like Fast Accurate Search Tool
biogrep
bioperl
Perl tools for bioinformatics - Core modules
bioperl-db
Perl tools for bioinformatics - Perl API that accesses the BioSQL schema
bioperl-network
Perl tools for bioinformatics - Analysis of protein-protein interaction networks
bioperl-run
Perl tools for bioinformatics - Analysis run modules
biopython
Biopython - Python modules for computational molecular biology
biosql
A generic bioinformatics relational database model
blat
The BLAST-Like Alignment Tool, a fast genomic sequence aligner
bowtie
An ultrafast memory-efficient short read aligner
bwa
Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner
cd-hit
clustal-omega
clustalw
General purpose multiple alignment program for DNA and proteins
clustalw-mpi
A parallel (MPI) implemention of the Clustal-W general purpose multiple alignment algorithm
clustalx
Graphical interface for the ClustalW multiple alignment program
cutg
Codon usage tables calculated from GenBank
dialign-tx
Greedy and progressive approaches for segment-based multiple sequence alignment
dialign2
elph
Estimated Locations of Pattern Hits - Motif finder program
embassy
A meta-package for installing all EMBASSY packages (EMBOSS add-ons)
embassy-cbstools
EMBOSS wrappers for applications from the CBS group
embassy-clustalomega
embassy-domainatrix
Protein domain analysis add-on package for EMBOSS
embassy-domalign
Protein domain alignment add-on package for EMBOSS
embassy-domsearch
Protein domain search add-on package for EMBOSS
embassy-emnu
EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications
embassy-esim4
EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA
embassy-hmmer
EMBOSS wrappers for HMMER - Biological sequence analysis with profile HMMs
embassy-iprscan
InterProScan motif detection add-on package for EMBOSS
embassy-mse
EMBOSS integrated version of MSE - Multiple Sequence Screen Editor
embassy-phylipnew
EMBOSS integrated version of PHYLIP - The Phylogeny Inference Package
embassy-signature
Protein signature add-on package for EMBOSS
embassy-structure
Protein structure add-on package for EMBOSS
embassy-topo
EMBOSS integrated version of TOPO - Transmembrane protein display
embassy-vienna
EMBOSS integrated version of the Vienna RNA package - RNA folding
emboss
The European Molecular Biology Open Software Suite - A sequence analysis package
eugene
Eukaryotic gene predictor
exonerate
exonerate is a generic tool for pairwise sequence comparison
fasta
FASTA is a DNA and Protein sequence alignment software package
fasttree
Fast inference of approximately-maximum-likelihood phylogenetic trees
fastx_toolkit
finchtv
A cross-platform graphical viewer for chromatogram files.
foldingathome
Folding@Home is a distributed computing project for protein folding.
glimmer
An HMM-based microbial gene finding system from TIGR
glimmerhmm
An eukaryotic gene finding system from TIGR
gmap
A Genomic Mapping and Alignment Program for mRNA and EST Sequences
hmmer
Sequence analysis using profile hidden Markov models
iedera
infernal
Inference of RNA alignments
iqpnni
Important Quartet Puzzling and NNI Operation
kalign
Global and progressive multiple sequence alignment
kallisto
lagan
LAGAN, Multi-LAGAN, Shuffle-LAGAN, Supermap: Whole-genome multiple alignment of genomic DNA
libgtextutils
mafft
Multiple sequence alignments using a variety of algorithms
maq
Mapping and Assembly with Qualities - mapping Solexa and SOLiD reads to reference sequences
maqview
GUI for sci-biology/maq, a short read mapping assembler
mcl
mosaik
A reference-guided aligner for next-generation sequencing technologies
mothur
A suite of algorithms for ecological bioinformatics
mrbayes
Bayesian Inference of Phylogeny
mummer
A rapid whole genome aligner
muscle
Multiple sequence comparison by log-expectation
newick-utils
pals
Pairwise Aligner for Long Sequences
paml
Phylogenetic Analysis by Maximum Likelihood
phylip
PHYLIP - The PHYLogeny Inference Package
phyml
Estimation of large phylogenies by maximum likelihood
piler
Analysis of repetitive DNA found in genome sequences
pilercr
Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
plink
Whole genome association analysis toolset
poa
Fast multiple sequence alignments using partial-order graphs
prank
Probabilistic Alignment Kit
primer3
Design primers for PCR reactions.
prints
A protein motif fingerprint database
probcons
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
prodigal
profphd
prosite
A protein families and domains database
pysam
qrna
Prototype ncRNA genefinder
raxml
A Program for Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
rebase
A restriction enzyme database
recon
rnaview
Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
samtools
SAM (Sequence Alignment/Map), a format for storing large nucleotide sequence alignments
seaview
A graphical multiple sequence alignment editor
seqan
sibsim4
A rewrite and improvement upon sim4, a DNA-mRNA aligner
sim4
A program to align cDNA and genomic DNA
STAR
stride
A program for protein secondary structure assignment from atomic coordinates.
t-coffee
A multiple sequence alignment package
tree-puzzle
Maximum likelihood analysis for nucleotide, amino acid, and two-state data.
treeviewx
A phylogenetic tree viewer
trf
Tandem Repeats Finder
trnascan-se
tRNA detection in large-scale genome sequences
uchime
ucsc-genome-browser
The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
unafold
update-blastdb
vcftools
velvet
A sequence assembler for very short reads
wise
Intelligent algorithms for DNA searches
yass