147 Packages in sci-biology

Portage Tree » sci-biology

Click the package name to view details, versions available and change logs.

ApE
A Plasmid Editor - Versions: 2.0.7-r1 (ApE)
GBrowse
Generic Model Organism Database Project - The Generic Genome Browser - Versions: 2.48-r1 (|| ( Artistic GPL-1+ ))
aaindex
Amino acid indices and similarity matrices - Versions: 9.1-r1 (public-domain)
abyss
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - Versions: 2.0.2-r1 (abyss)
allpathslg
De novo assembly of whole-genome shotgun microreads - Versions: 52488-r2 (MIT)
amap
Protein multiple-alignment-based sequence annealing - Versions: 2.2-r3 (GPL-2)
amos
A Modular, Open-Source whole genome assembler - Versions: 3.1.0-r3 (Artistic)
arb
Tools for DNA/RNA sequence database handling and phylogenetic analysis - Versions: 5.2, 5.3, 5.1-r1 (arb)
ariadne
Protein sequences and profiles comparison - Versions: 1.3-r3 (ARIADNE)
augustus
Eukaryotic gene predictor - Versions: 2.5.5 (Artistic)
bamtools
A programmer's API and an end-user's toolkit for handling BAM files - Versions: 2.4.1 (MIT)
beast-mcmc
Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences - Versions: 9999, 1.7.5-r1 (LGPL-3)
bedtools
Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats - Versions: 2.26.0 (GPL-2)
bfast
Blat-like Fast Accurate Search Tool - Versions: 0.7.0a (GPL-2)
biogrep
Multithreaded tool for matching large sets of patterns against biosequence DBs - Versions: 1.0-r2 (GPL-2)
biopandas
Molecular Structures in Pandas DataFrames - Versions: 0.1.4 (BSD)
bioperl
Perl tools for bioinformatics - Core modules - Versions: 9999-r1, 1.6.9 (Artistic GPL-2)
bioperl-db
Perl tools for bioinformatics - Perl API that accesses the BioSQL schema - Versions: 1.6.9, 9999-r1 (|| ( Artistic GPL-1+ ))
bioperl-network
Perl tools for bioinformatics - Analysis of protein-protein interaction networks - Versions: 9999-r1, 1.6.9 (Artistic GPL-2)
bioperl-run
Perl wrapper modules for key bioinformatics applications - Versions: 1.6.9, 9999-r1 (|| ( Artistic GPL-1+ ))
biopython
Python modules for computational molecular biology - Versions: 1.68 (HPND)
bioruby
An integrated environment for bioinformatics using the Ruby language - Versions: 1.4.3.0001-r1, 9999 (Ruby)
biosql
A generic bioinformatics relational database model - Versions: 1.0.1-r1 (LGPL-3)
blat
The BLAST-Like Alignment Tool, a fast genomic sequence aligner - Versions: 34-r2 (blat)
blossoc
A linkage disequilibrium association mapping tool - Versions: 1.4.0-r1 (GPL-3)
bowtie
Popular short read aligner for Next-generation sequencing data - Versions: 1.1.2, 2.2.9, 1.1.2-r1, 2.2.6 (Artistic)
bwa
Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner - Versions: 0.7.15, 0.7.12 (GPL-3)
cd-hit
Clustering Database at High Identity with Tolerance - Versions: 4.6.6 (GPL-2)
clustal-omega
Scalable multiple alignment of protein sequences - Versions: 1.2.3, 1.2.1, 1.2.4 (GPL-2)
clustalw
General purpose multiple alignment program for DNA and proteins - Versions: 1.83-r4, 2.1-r1 (clustalw)
clustalw-mpi
An MPI implemention of the ClustalW general purpose multiple alignment algorithm - Versions: 0.13-r2 (public-domain)
clustalx
Graphical interface for the ClustalW multiple alignment program - Versions: 2.1-r2, 2.1-r1 (GPL-3 LGPL-3)
consed
A genome sequence finishing program - Versions: 29 (phrap)
cufflinks
Transcript assembly and differential expression/regulation for RNA-Seq - Versions: 2.2.1-r2 (Artistic)
cutg
Codon usage tables calculated from GenBank - Versions: 160-r1 (public-domain)
dialign-tx
Greedy and progressive approaches for segment-based multiple sequence alignment - Versions: 1.0.2-r1 (LGPL-2.1)
dialign2
Multiple sequence alignment - Versions: 2.2.1 (LGPL-2.1)
diya
Do It Yourself Annotation, tools & libraries for sequence assembly & annotation - Versions: 1.0_rc4 (GPL-3)
elph
Estimated Locations of Pattern Hits - Motif finder program - Versions: 1.0.1-r1 (Artistic)
embassy
A meta-package for installing all EMBASSY packages (EMBOSS add-ons) - Versions: 6.6.0-r1 (freedist)
embassy-cbstools
EMBOSS integrated version of Applications from the CBS group - Versions: 1.0.0.660 (LGPL-2 GPL-2)
embassy-clustalomega
EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment - Versions: 1.1.0.660 (LGPL-2 GPL-2)
embassy-domainatrix
EMBOSS integrated version of Protein domain analysis add-on package - Versions: 0.1.660 (LGPL-2 GPL-2)
embassy-domalign
EMBOSS integrated version of Protein domain alignment add-on package - Versions: 0.1.660 (LGPL-2 GPL-2)
embassy-domsearch
EMBOSS integrated version of Protein domain search add-on package - Versions: 0.1.660 (LGPL-2 GPL-2)
embassy-emnu
EMBOSS integrated version of Simple menu of EMBOSS applications - Versions: 1.05.660 (LGPL-2 GPL-2)
embassy-esim4
EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA - Versions: 1.0.0.660 (LGPL-2 GPL-2)
embassy-hmmer
EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs - Versions: 2.3.2.660 (LGPL-2 GPL-2)
embassy-iprscan
EMBOSS integrated version of InterProScan motif detection add-on package - Versions: 4.3.1.660 (LGPL-2 GPL-2)
embassy-meme
EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation - Versions: 4.7.660 (LGPL-2 GPL-2)
embassy-mse
EMBOSS integrated version of MSE - Multiple Sequence Screen Editor - Versions: 3.0.0.660 (LGPL-2 GPL-2)
embassy-phylipnew
EMBOSS integrated version of The Phylogeny Inference Package - Versions: 3.69.660 (LGPL-2 GPL-2 freedist)
embassy-signature
EMBOSS integrated version of Protein signature add-on package - Versions: 0.1.660 (LGPL-2 GPL-2)
embassy-structure
EMBOSS integrated version of Protein structure add-on package - Versions: 0.1.660 (LGPL-2 GPL-2)
embassy-topo
EMBOSS integrated version of Transmembrane protein display - Versions: 2.0.660 (LGPL-2 GPL-2)
embassy-vienna
EMBOSS integrated version of Vienna RNA package - RNA folding - Versions: 1.7.2.660 (LGPL-2 GPL-2)
emboss
The European Molecular Biology Open Software Suite - A sequence analysis package - Versions: 6.6.0-r1 (LGPL-2 GPL-2 Apache-2.0 GPL-3+ CC-BY-3.0)
eugene
Eukaryotic gene predictor - Versions: 4.1, 4.1d (Artistic)
exonerate
Generic tool for pairwise sequence comparison - Versions: 2.2.0-r2 (GPL-3)
express
Streaming RNA-Seq Analysis - Versions: 0.9.5-r1, 1.5.1 (Artistic)
fasta
FASTA is a DNA and Protein sequence alignment software package - Versions: 35.4.10, 36.3.5e (fasta)
fasttree
Fast inference of approximately-maximum-likelihood phylogenetic trees - Versions: 2.1.8, 2.1.7 (GPL-2)
finchtv
Graphical viewer for chromatogram files - Versions: 1.3.1-r3, 1.3.1-r2 (finchtv)
foldingathome
Folding@Home is a distributed computing project for protein folding - Versions: 7.4.4-r1 (FAH-EULA-2014 FAH-special-permission)
gatk
The Genome Analysis Toolkit - Versions: 2.4, 9999 (MIT)
gibbs
Identify motifs, conserved regions, in DNA or protein sequences - Versions: 3.1 (GPL-2)
glimmer
An HMM-based microbial gene finding system from TIGR - Versions: 3.02-r3, 3.02b (Artistic)
glimmerhmm
A eukaryotic gene finding system from TIGR - Versions: 3.0.1-r1 (Artistic)
gmap
A Genomic Mapping and Alignment Program for mRNA and EST Sequences - Versions: 2015.12.31.5 (gmap)
goby
A DNA sequencing data management framework - Versions: 1.9.7.3-r1, 1.9.8.1-r1 (GPL-3 LGPL-3)
goby-cpp
A DNA sequencing data management framework - C/C++ API - Versions: 1.9.7.3, 2.0.1, 1.9.8.1 (GPL-3)
hmmer
Sequence analysis using profile hidden Markov models - Versions: 3.1_beta2, 2.3.2-r4, 2.3.2-r3 (GPL-3)
iedera
A subset seed design tool for DNA sequence alignment - Versions: 1.04, 1.05-r1 (GPL-2)
infernal
Inference of RNA alignments - Versions: 1.0.2-r1 (GPL-3)
iqpnni
Important Quartet Puzzling and NNI Operation - Versions: 3.3.2-r1 (GPL-2)
kalign
Global and progressive multiple sequence alignment - Versions: 2.03-r2 (GPL-2)
lagan
The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA - Versions: 2.0-r3 (GPL-2)
last
Genome-scale comparison of biological sequences - Versions: 299-r1, 230 (GPL-3)
mafft
Multiple sequence alignments using a variety of algorithms - Versions: 7.305, 7.050, 7.215 (BSD)
mammoth
MAtching Molecular Models Obtained from THeory - Versions: 1.0-r1 (mammoth)
maq
Mapping and Assembly with Qualities, mapping NGS reads to reference genomes - Versions: 0.7.1-r2 (GPL-3)
maqview
GUI for sci-biology/maq, a short read mapping assembler - Versions: 0.2.5-r3 (GPL-3)
mcl
A Markov Cluster Algorithm implementation - Versions: 08.312, 14.137, 12.135 (GPL-2)
meme
The MEME/MAST system - Motif discovery and search - Versions: 4.11.2_p2 (meme)
mira
Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina - Versions: 4.0.2 (GPL-2)
mosaik
A reference-guided aligner for next-generation sequencing technologies - Versions: 2.2.30 (GPL-2)
mothur
A suite of algorithms for ecological bioinformatics - Versions: 1.27.0-r1 (GPL-3)
mrbayes
Bayesian Inference of Phylogeny - Versions: 3.1.2-r1, 3.1.2-r2 (GPL-2)
mummer
A rapid whole genome aligner - Versions: 3.23 (Artistic)
muscle
Multiple sequence comparison by log-expectation - Versions: 3.8.31 (public-domain)
ncbi-tools
Development toolkit and applications for computational biology, including BLAST - Versions: 2.2.26-r2 (public-domain)
newick-utils
Tools for processing phylogenetic trees - Versions: 1.6 (BSD)
njplot
A phylogenetic tree drawing program which supports tree rooting - Versions: 2.3-r2 (public-domain)
pals
Pairwise Aligner for Long Sequences - Versions: 1.0-r1 (public-domain)
paml
Phylogenetic Analysis by Maximum Likelihood - Versions: 4.4c-r1 (free-noncomm)
phrap
Shotgun assembly and alignment utilities - Versions: 1.080812-r2 (phrap)
phred
A base caller for Sanger DNA sequencing - Versions: 071220-r1 (phrap)
phylip
The PHYLogeny Inference Package - Versions: 3.696-r1, 3.69-r1 (BSD-2)
phyml
Estimation of large phylogenies by maximum likelihood - Versions: 2.4.5-r3 (GPL-2)
picard
Java-based command-line utilities that manipulate SAM files - Versions: 1.103 (Apache-2.0)
piler
Analysis of repetitive DNA found in genome sequences - Versions: 1.0-r1 (public-domain)
pilercr
Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) - Versions: 1.0-r1 (public-domain)
plink
Whole genome association analysis toolset - Versions: 1.90_pre140514, 1.07-r1 (GPL-2)
poa
Fast multiple sequence alignments using partial-order graphs - Versions: 2-r1 (GPL-2)
prank
Probabilistic Alignment Kit - Versions: 140603 (GPL-3)
primer3
Primer Design for PCR reactions - Versions: 2.3.5, 2.3.7, 2.3.6 (GPL-2)
prints
A protein motif fingerprint database - Versions: 39.0-r1 (public-domain)
probcons
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences - Versions: 1.12-r1 (public-domain)
prodigal
Prokaryotic Dynamic Programming Genefinding Algorithm - Versions: 2.6.3 (GPL-3)
profphd
Secondary structure and solvent accessibility predictor - Versions: 1.0.39, 1.0.40 (GPL-2)
prosite
A protein families and domains database - Versions: 2017.02 (swiss-prot)
psipred
Protein Secondary Structure Prediction - Versions: 3.3, 3.4, 3.2.1, 3.5 (psipred)
pysam
Python interface for the SAM/BAM sequence alignment and mapping format - Versions: 0.9.0 (MIT)
qrna
Prototype ncRNA genefinder - Versions: 2.0.3c-r2 (GPL-2)
raxml
Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees - Versions: 7.2.6 (GPL-2)
rebase
A restriction enzyme database - Versions: 1703, 1704, 1701, 1702 (public-domain)
recon
Automated de novo identification of repeat families from genomic sequences - Versions: 1.08 (GPL-2)
repeatmasker
Screen DNA sequences for interspersed repeats and low complexity DNA - Versions: 4.0.1 (OSL-2.1)
repeatmasker-libraries
A special version of RepBase used by RepeatMasker - Versions: 20120418 (all-rights-reserved)
rmblast
RepeatMasker compatible version of NCBI BLAST+ - Versions: 1.2-r1 (OSL-2.1)
rnaview
Generates 2D displays of RNA/DNA secondary structures with tertiary interactions - Versions: 20040713-r4 (public-domain)
samtools
Utilities for analysing and manipulating the SAM/BAM alignment formats - Versions: 0.1.20-r3, 0.1.19-r2, 1.3-r1, 1.1, 1.0-r1, 0.1.12, 1.0, 1.2 (MIT)
seaview
A graphical multiple sequence alignment editor - Versions: 4.6, 4.5.4, 4.3.5 (public-domain)
seqan
C++ Sequence Analysis Library - Versions: 1.4.2-r1, 2.2.0-r1 (BSD GPL-3)
shrimp
SHort Read Mapping Package - Versions: 2.0.1, 2.2.3 (shrimp)
sibsim4
A rewrite and improvement upon sim4, a DNA-mRNA aligner - Versions: 0.20 (GPL-2)
sim4
A program to align cDNA and genomic DNA - Versions: 20030921-r2 (GPL-2)
snpfile
A library and API for manipulating large SNP datasets - Versions: 2.0.1-r2 (GPL-3)
stride
Protein secondary structure assignment from atomic coordinates - Versions: 20011129-r1 (STRIDE)
t-coffee
A multiple sequence alignment package - Versions: 9.03.1318-r1, 11.00-r1 (GPL-2)
tophat
Python-based splice junction mapper for RNA-Seq reads using bowtie2 - Versions: 2.1.1-r4 (Artistic)
transfac
A database of eucaryotic transcription factors - Versions: 3.2-r1 (public-domain)
tree-puzzle
Maximum likelihood analysis for nucleotide, amino acid, and two-state data - Versions: 5.2 (GPL-2)
treeviewx
A phylogenetic tree viewer - Versions: 0.5.1-r3 (GPL-2)
trf
Tandem Repeats Finder - Versions: 4.04-r1 (trf)
trnascan-se
tRNA detection in large-scale genome sequences - Versions: 1.31, 1.23-r2 (GPL-2)
uchime
Fast, accurate chimera detection - Versions: 4.2.40 (public-domain)
ucsc-genome-browser
The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath - Versions: 260 (blat)
unafold
Unified Nucleic Acid Folding and hybridization package - Versions: 3.8-r1 (unafold)
update-blastdb
update_blastdb.pl for local blast db maintainance - Versions: 12.0.0 (public-domain)
vaal
Algorithm for detecting SNPs, indels, and other polymorphisms - Versions: 46233-r2 (Whitehead-MIT)
vcftools
Tools for working with VCF (Variant Call Format) files - Versions: 0.1.14 (LGPL-3)
velvet
A sequence assembler for very short reads - Versions: 1.0.18-r1, 1.2.10 (GPL-2)
vienna-rna
RNA secondary structure prediction and comparison - Versions: 2.1.1, 2.1.8 (vienna-rna)
wgs-assembler
The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG - Versions: 7.0-r1 (GPL-2)
wise
Intelligent algorithms for DNA searches - Versions: 2.4.0_alpha (BSD)
yass
Genomic similarity search with multiple transition constrained spaced seeds - Versions: 1.14-r2 (GPL-2)
comments powered by Disqus