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 |
| Cufflinks | bio/cufflinks | Transcript assembly and abundance estimation for RNA-Seq | 2.2.0 |
| 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 |