The Bioinformatics Source Release Collection

BioSRC Package List

This is a list of all the packages that are currently present in BioSRC. This list is automatically updated weekly to reflect the latest software versions or package additions. The "BioSRC Name" of a package is the one that you would use to install the package via BioSRC, i.e. make -C pkg/bio/hmmer install. The "Name" of the package is its canonical name.

Last update: Mon 27 Oct 2014 08:00:05 PM GMT

Name BioSRC Name Description Version
argtable libs/argtable An ANSI C command-line parser 2.13
bambamc libs/bambamc A C implementation of name-collating BAM file input and output 0.0.50
BamTools bio/bamtools A library and toolkit for handling BAM files 2.3.0
BEAGLE libs/beagle-lib A library for evaluating the likelihoodof sequence evolution on trees 2.1.2
BEDTools bio/bedtools A swiss army knife for genome arithmetic 2.20.0
BFAST bio/bfast Blat-like Fast Accurate Search Tool 0.7.0a
Bismark bio/bismark A bisulfite read mapper and methylation caller 0.10.1
Boost libs/boost A diverse collection of C++ libraries 1.55.0
Bowtie 2 bio/bowtie Fast and sensitive read alignment 2.2.1
Breakway bio/breakway Report structural variation breakpoints in genomic data 0.7.1
Burrows-Wheeler Aligner bio/bwa Map low-divergent sequences against a large reference genome 0.7.8
CD-HIT bio/cd-hit Cluster and compare protein or nucleotide sequences 4.6.1
Clustal Omega bio/clustal-omega The last alignment program you will ever need 1.2.1
Clustal W bio/clustalw Multiple alignment of nucleic acid and protein sequences 2.1
CS-BLAST bio/csblast Context-specific sequence profiels for homology searching 2.2.4
datamash tools/datamash Perform absic numeric, textual and statistical operations 1.0.5
DNAA bio/dnaa DNA analysis package 0.1.2
e-PCR bio/e-pcr Electronic PCR 2.3.12
Eigen libs/eigen A C++ template library for linear algebra 3.2.1
EMBOSS bio/emboss A collection of molecular biology packages 6.6.0
FastTree bio/fasttree Fast approximation of maximum-likelihood phylogenetic trees 2.1.7
FASTX-Toolkit bio/fastx-toolkit FASTQ/A short-reads pre-processing tools 0.0.14
FSA bio/fsa Fast statistical alignment 1.15.9
The GNU Compiler Collection dev/gcc GNU Compiler Collection 4.9.0
dbm libs/gdbm Hash library of database functions compatible with traditional dbm 1.11
GNU Linear Programming Kit libs/glpk GNU Linear Programming Kit, supporting the MathProg language 4.53
The GNU Scientific Library libs/gsl Numerical library for C and C++ 1.16
HMMR bio/hmmer Biosequence analysis using profile hidden Markov models 3.1b1
HyPhy bio/hyphy Hypothesis testing using phylogenies 2.2
Jellyfish bio/jellyfish Fast, parallel k-mer counting for DNA 2.1.3
Kraken bio/kraken Taxonomic sequence classification system 0.10.4
libGTextUtils libs/libgtextutils A library of various text processing functions 0.7
MACS bio/macs Model-based analysis for ChIP-Seq 1.4.2
MAFFT bio/mafft A multiple sequence alignment program 7.130
MCSim tools/mcsim Monte Carlo simulation and analysis 5.5.0
MELTING bio/melting Temperature computations for a nucleic acid duplex 5.1.2
MOODS bio/moods Motif occurrence detection suite 1.0.1
MrBayes bio/mrbayes Bayesian inference of phylogeny 3.2.2
MUMmer bio/mummer Ultra-fast alignment of large-scale sequences 3.23
BLAST+ bio/ncbi-blast Basic Local Alignment Search Tool 2.2.29
The Newick Utilities bio/newick-utils Command-line tools for processing phylogenetic trees 1.6
NLopt libs/nlopt A library for nonlinear optimization 2.4.1
OMA bio/oma Large-scale orthology inference 0.99u.3
PAGAN bio/pagan-msa A general-purpose method for the alignment of sequence graphs 20121025
Parallel tools/parallel Build and execute command lines in parallel 20140322
Bioperl libs/perl-bioperl Perl code which is useful in biology 1.6.923
Ensembl libs/perl-ensembl Ensembl Perl API 75
Ensembl Compara libs/perl-ensembl-compara Ensembl Compara Perl API 75
Ensembl Funcgen libs/perl-ensembl-funcgen Ensembl Funcgen Perl API 75
Ensembl Variation libs/perl-ensembl-variation Ensembl Variation Perl API 75
PfamScan bio/pfamscan Search Pfam locally 2013-10-15
PhyML bio/phyml Estimate phylogenies by maximum likelihood 20140223
plotutils tools/plotutils Plotting utilities and library 2.6
PRANK bio/prank-msa A probabilistic multiple alignment program 140110
Primer3 bio/primer3 Design PCR primers 2.3.6
PROVEAN bio/provean Protein variation effect analyzer 1.1.5
Pscan bio/pscan Motif discovery in sequences 1.3
Python dev/python A general-purpose, high-level programming language 3.4.0
Biopython libs/python-biopython A set of Python modules for biological computation 1.63
NetworkX libs/python-networkx Python library for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks 1.8.1
NetworkX (Python 2) libs/python-networkx Python library for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks 1.8.1
NumPy libs/python-numpy Numerical python 1.8.0
Pandas libs/python-pandas Python data analysis library 0.13.1
SciPy libs/python-scipy A mathematical library for Python 0.13.3
SciPy (Python 2) libs/python-scipy A mathematical library for Python 0.13.3
setuptools libs/python-setuptools Easily download, build, install, upgrade and uninstall Python packages 3.6
setuptools libs/python-setuptools Easily download, build, install, upgrade and uninstall Python packages 3.6
SQLAlchemy libs/python-sqlalchemy The Python SQL toolkit and Object Relational Mapper 0.9.4
Python 2 dev/python2 A general-purpose, high-level programming language (Version 2) 2.7.7
Biopython (Python 2) libs/python2-biopython A set of Python modules for biological computation 1.63
Dateutil (Python 2) libs/python2-dateutil Extensions to the standard Python datetime module 2.2
HTSeq libs/python2-htseq A framework to process and analyze high-throughput sequencing data 0.6.0
NumPy (Python 2) libs/python2-numpy Numerical python 1.8.0
Pandas (Python 2) libs/python2-pandas Python data analysis library 0.13.1
SQLAlchemy (Python 2) libs/python2-sqlalchemy The Python SQL toolkit and Object Relational Mapper 0.9.4
QmmRAxML bio/qmmraxml Q-matrix mixture RAxML 2.0
Quake bio/quake Correct Illumina substitution sequencing errors 0.3.5
R dev/r Environment for statistical computing and graphics 3.1.0
RAxML bio/raxml Sequential and parallel Maximum Likelihood inference of phylogenetic trees 8.0.7
REAPR bio/reapr Recognising errors in assemblies using paired reads 1.0.17
RNAz bio/rnaz Predicting structural noncoding RNAs 2.1
SAMtools bio/samtools Utilities for manipulating alignments in the SAM format 0.1.19
SeqAn libs/seqan A C++ library for the analysis of sequences 1.4.1
SeqSuite bio/seqsuite A suite of sequence analysis programs 2013-12-03
Seqtk bio/seqtk A toolkit for processing sequences in FASTA/Q formats 1.0
SMALT bio/smalt A mapper for DNA sequencing reads 0.7.6
SNP-o-matic bio/snpomatic A fast, stringent short-read mapping software r14
sparsehash libs/sparsehash An extremely memory-efficient hash_map implementation 2.0.2
T-Coffee bio/t-coffee A multiple sequence alignment package 10.00.r1613
Tabix bio/tabix Generic indexer for TAB-delimited genome position files 0.2.6
TopHat bio/tophat A fast splice junction mapper for RNA-Seq reads 2.0.11
TreeBeST bio/treebest Tree-building guided by species trees 1.9.2
trimAl bio/trimal A tool for automated alignment trimming 1.2rev59
Units tools/units Conversion between thousands of scales 2.02
Wdiff tools/wdiff Word difference finder 1.2.1
Weeder bio/weeder Motif discovery in sequences from co-regulated genes 2.0
WeederH bio/weederh Find conserved regulatory regions in homologous sequences 1.0
zeptodb tools/zeptodb Command-line DBM tools 2.0.2b