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HPCC has an extensive list of software installed. To use a piece of software, an appropriate module must be loaded.This page reviews how to use modules before providing a list of installed software.

Modules

A module manages environment variables needed to load a particular piece of software. The login process loads a few modules by default for HPCC users. The default loaded modules include the GNU compilers, the OpenMPI communication library, MATLAB and R.

  • To see a list of modules that are currently loaded, type "module list"

  • To see a list of modules that are available to be loaded, type "module avail"
  • To see what environment variables would be set/changed if you load a specific module, type "module show <module_name>"
  • To load a module, type "module load <module_name>"
  • To unload a module, type "module unload <module_name>"
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A video tutorial of how to use the modules can be found here: Video Tutorial - Modules

List of installed software

The following is a list of installed software, sorted by application area. If you require a software title that is not installed, you may install it locally to your home directory. Alternatively, if the software will benefit other users at HPCC, a request can be submitted to http://www.hpcc.msu.edu/contact to request a more global installation by HPCC staff.

Bioinformatics Software

Module Name

Version

Brief Description

A5

20120518, 20130326

A genome assembly pipeline for bacteria and archaea that automates as much data cleaning and parameter selection as possible.

ABySS

1.2.5, 1.3.2, 1.3.3, 1.3.4, 1.3.5, 1.3.6, 1.5.1

A de novo parallel, paired-end sequence assembler designed for short reads.

agalma

0.3.3

Agalma is a set of analysis pipelines for phylogenomic analyses. It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data.

AlignACE

2004

 

ALLPATHS

41313, 44837, 47417

Whole genome assembler for short reads.

AMOS

3.1.0

AMOS - A Modular Open-Source whole genome assembler.

AmpliconNoise

1.25

A whole genome association analysis toolset for the analysis of genotype/phenotype data.

AmpliCopywriter

0.46

analysis

0.8.1

C++ software for evolutionary genetic analysis.

annovar

20130417, 20130514, 20140409

A tool to use up-to-date information to functionally annotate genetic variants from a variety of genomes.

aragorn

2.36c

tRNA and tmRNA detection.

ARB

5.5, 6.0.2, 8210

A database oriented graphical package for building phylogeny trees

augustus

2.5.5, 2.7.0, 3.1.0

Predicts genes in eukaryotic genome sequences.

autoadapt

0.2

Easy to use wrapper than utilizes cutadapt and fastqc to auto-detect and remove adapter sequences.

bamaddrg

20140611

bamaddrg: adds read groups to input BAM files, streams BAM output on stdout.

bam-readcount

0.7.4

count DNA sequence reads in BAM files

BamBam

20130422, 20130423, 20130708, 20130717

Several simple-to-use tools to facilitate NGS analysis.

BAMseek

20110724

A Large File Viewer for BAM and SAM alignment files.

BAMTools

1.0.2, 2.2.3

A fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

BarraCUDA

r259

GPU capable short read aligner based on BWA.

BBMap

33.34, 33.57

short read aligner, and other bioinformatic tools.

bcbb

20130430

 

bcftools

0.0.1, 1.2

Utilities for variant calling and manipulating VCFs and BCFs. Includes functionality of HTSlib

Beagle

4.0

A general purpose library for evaluating the likelihood of sequence evolution of trees.

beagle-lib

2.1.2

general purpose library for evaluating the likelihood of sequence evolution on trees.

BEDOPS

2.4.5

a fast, highly scalable and easily-parallelizable genome analysis toolkit.

BEDTools

2.13.1, 2.17.0, 2.24.0

A utilities package to address common genomic data manipulation tasks.

bedUtils

20120103

Python utilities for handling BED format files.

BELT

1.0.1

 

BER

20051118

BLAST-Extend-Repraze (BER) is a package for identifying potential frameshifts or point mutations in a given open reading frame (ORF).

BFAST

0.7.0a

BLAT-like tool that facilitates the fast mapping of short reads to reference sequences.

biolite

0.3.1

 

biomformat

0.9.3, 1.2.0, 1.31

A Python module for comparative genomics.

Bioperl

1.6.1, 1.6.901, 1.6.923

A collection of Perl modules for bioinformatics processing and analysis.

biopieces

0.48

A bioinformatics framework for adding tools to a workflow path.

BioGraPy

1.0

biological graphic tool in Python.

Biopython

1.58, 1.61, 1.65

Python tools for biological computation.

Biorithm

1.1

Biorithm is a C++ package that includes several libraries and software tools to analyze data in molecular systems biology.

bioscriptsConvert

0.4

Biopython scripts for converting molecular sequences between formats.

BLAS

20110922

Parallel Visualization Program.

blasr

1.3.1

Pacbio alignment tool

BLAST

2.2.22, 2.2.25

Basic Local Alignment Search Tool

BLAST+

2.2.25, 2.2.26, 2.2.27, 2.2.28, 2.2.29, 2.2.30, 2.2.31

Basic Local Alignment Search Tool

blast2go

3.0

a bioinformatics platform for high-quality functional annotation and analysis of genomic datasets.

BLAT

34, 35, 36

Basic Local Alignment Tool

bowtie

0.12.3, 0.12.7, 0.12.8, 1.0.0, 2.2.6

A fast memory-efficient short-read aligner

bowtie2

2.1.0, 2.2.0, 2.2.1, 2.2.3, 2.2.6

A fast memory-efficient short-read aligner

BreakDancer

1.1.2

a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

breseq

0.16, 0.23, 0.26

a computational pipeline for the analysis of short-read re-sequencing data.

BTLib

0.19

A collection of Perl modules for ESTScan.

bwa

0.6.0, 0.7.5a.r405, 0.7.5a.r428, 0.7.7.r441

BWA aligns relatively short nucleotide sequences against a long reference sequence

bxPython

2.7

A Python module for manipulating multiple sequence alignments.

CAP3

3.0

A genome assembler.

cdbtools

1.0, 20110519

Fast file indexing and retrieval tool.

CDHIT

4.5.6, 4.6.1, 4.6.1b, 4.6.1c

A very widely used program for clustering and comparing large sets of protein or nucleotide sequences

CEGMA

2.3, 2.4

A computational method for building a highly reliable set of gene annotations in the absence of experimental data.

censor

4.2.22

FASTX is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

ChimeraSlayer

20110519

 

circonspect

0.2.6

Circonspect is a bioinformatic tool to produce contig spectra, useful for the estimating viral diversity in metagenomes.

CIRCOS

0.55

Displays data in a circular format.

Circuitscape

3.5.7

Uses electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes.

clearcut

1.3

Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm.

ClustalO

1.1.0

A sequence aligner based on ClustalW with improved scalability and speed.

ClustalW

2.1

Multiple alignment of nucleic acid and protein sequences.

cluster3

1.50

A computational and graphical environment for analyzing data from DNA microarray experiments, or other genomic datasets.

CNVnator

0.2.7

A tool for CNV discovery and genotyping from depth of read mapping.

cobrapy

20140530

COBRApy is a package for constraints-based modeling of biological networks

consed

20.0, 22.0

A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

cortex

0.04c

Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data.

cortexVar

1.0.5.21

A tool for genome assembly and variation analysis from sequence data.

cudaMEME

3.0.12

GPU version of the MEME motif discovery tool

cufflinks

0.9.3, 1.1.0, 1.3.0, 2.0.0, 2.0.2, 2.1.1, 2.2.0, 2.2.1

Transcript assembly, differential expression, and differential regulation for RNA-Seq

curtain

0.2.1

A java wrapper around next-gen assemblers such as Velvet, which allow incremental introduction of read-pair info into the assembly process

delly

0.5.5

Bioinformatics Structural Variant (SV) detection

DendroPy

3.12.0

 

DETONATE

20140123

DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

DIAL

20110606

DIAL is a collection of programs to automate the discovery of alleles for species where we lack a reference sequence. The SNPs/alleles are specifically selected for a low error rate of genotyping assays.

DIALIGN

2.2.1

A software program for multiple sequence alignment.

diffReps

1.55.1

Finding differential chromatin modification sites from ChIP-seq data.

DIYABC

0.7.2

A friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers.

docutils

0.11

 

eaUtils

1.1.2.7-537

Tools for processing FASTQ files.

Edena

3.131028

A very short-read de novo assembler.

EMBOSS

6.4.0, 6.5.7

Molecular BIology Software Suite.

emperor

0.9.1

 

ESTScan

3.0.3

Detects coding regions in DNA sequences, even if they are of low quality, and detects/corrects sequencing errors that lead to frameshifts.

ETE2

2.2.r1019

 

exonerate

2.2.0

A tool for pairwise sequence alignment.

eXpress

1.5.1

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

FaQCs

1.3

Quality trimming and QC reporting From LANL

fasta

36.3.6

FASTA management software

fasta36

36.3.6d

Improved Tools for Biological Sequence Analysis

fastPHASE

1.4.0

Haplotype reconstruction and estimating missing genotypes from population data.

FastQC

0.10.0, 0.10.1, 0.11.1, 0.11.2

A quality control tool for high throughput sequence data.

FastTree

2.1.3c, 2.1.7

 

FASTX

0.0.13, 0.0.14

FASTX is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

FFPred2

20130911

An integrated feature-based function prediction server for vertebrate proteomes.

flexbar

2.4

Barcode removal for MiSeq

Foldalign

2.1.1

Pairwise local or global RNA Structure and Sequence ALignment

freebayes

20130417, 20140521

FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.

FREEC

6.7

A tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data.

GAAS

0.17

A bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.

galaxy

1.0

Galaxy Metamodule loads

GATK

2.2.16, 2.5.2, 2.7.2, 3.1.1

Analysis package for next-gen resequencing data.

Gblastn

2.28

GPU version of the NCBI's Basic Local Alignment Search Tool for blastn

gdata

20131104

 

geneid

1.4.4

A program to predict genes in anonymous genomic sequences designed with a hierarchical structure.

GeneMarkES

2.3e

GeneMark-ES algorithm was designed for finding protein coding genes in eukaryotic genomes without training sets.

Genepop

4.1.2

A population genetics software package.

GenomeTools

1.4.1, 1.5.1, 1.5.3, 1.5.8

A collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named 'libgenometools' which consists of several modules.

GICL

20130726

Automates clustering and assembly of a large EST/mRNA dataset.

git-python

0.3.1

Python libraries for workign with git

glimmer

3.02

Glimmer is a system for finding genes in microbial DNA.

GMAP

20110914, 20111120, 20120421, 20121212, 20130205, 20130331.large, 20130714, 20130819

A genomic mapping and alignment program for mRNA and EST sequences.

GOperl

0.15

Perl modules for parsing and manipulating Gene Ontologies and Annotations.

gpuBLAST

1.1

GPU version of the NCBI's Basic Local Alignment Search Tool

h5py

2.1.3

The h5py package is a Pythonic interface to the HDF5 binary data format.

HHblits

2.0.16

Homology detection by iterative HMM-HMM comparison.

HMMER

2.3.2, 3.0, 3.1b1

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequnce alignments.

HOMER

20130715, 4.5

Hypergeometric Optimization of Motif EnRichment.

HTSeq

0.5.3, 0.5.3p9, 0.6.1

A Python package that provides tools for high-throughput sequencing analysis.

IDBAUD

1.1.0, 1.1.1

A iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

IGV

2.1.21

integrative genomics viewer

IGVTools

2.3.26

The igvtools utility provides a set of tools for pre-processing data files.

ima2

8.26.11

Isolation with Migration model for genetic data.

infernal

1.0.2, 1.1rc1

library for data formats

InSilicoSpectro

1.3.24

InSilicoSpectro is a proteomics open-source project intended to cover common operations in mass list file format conversions, protein sequence digestion, theoretical mass spectra computations, theoretical and experimental MS data matching, text/graphic display, peptide retention time predictions, etc.

iprscan

5.0.rc7, 5.1.44.0, 5.4.47.0, 5.44.0, 5.6.48.0

 

jellyfish

1.1.4

Model-based Analysis of ChIP-Seq (MACS), for identifying transcription factor binding sites.

jellyfish2

2.1.1

Fast memory efficient counting of kmers. Jellyfish2 has several enhancements of Jellyfish, and supports longer kmer sizes and better memory management.

jmodeltest2

2.1.4

Performs statistical selection of best-fit models of nucleotide substitution.

khmer

0.6.1, 0.7.1, 0.8.3, 042012, 082011, 08272012, 09062012, 1.0.1-rc2, 1.1

k-mer counting, filtering and graph traversal

KmerGenie

1.5397

KmerGenie detects the best k-mer length for de novo assembly.

LASTZ

1.03.02

LASTZ aligns DNA sequences using pairwise alignment

libSBML

5.10.0

A programming library to help you read, write, manipulate, translate, and validate SBML files and data streams.

libsequence

1.7.4

libsequence is a C++ library designed to aid writing applications for genomics and evolutionary genetics.

LOX

1.7

Employs Markov Chain Monte Carlo analysis to estimate levels of gene expression.

MACS

1.3.7

Model-based Analysis of ChIP-Seq (MACS), for identifying transcription factor binding sites.

MAKER

2.28, 2.31, 2.10

Allows eukarotic and prokaryotic genome projects to annotate their genomes and create databases

MAQ

0.7.1

Mapping and assembly qualities

maqview

0.2.5

Maqview is graphical read alignment viewer.

mcl

11335

A very efficient equence assembler

MCScanX

2

MCScan is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors. MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity and extends the software by incorporating 15 utility programs for display and further analyses.

MDscan

2004

 

MEME

4.4.0, 4.7.0, 4.9.1, 4.11.1

Motif-based sequence analysis tools

MetaSim

0.9.5

FASTX is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

MetaVelvet

1.2.02

Sequence assemble for very short reads in metagenomics.

migrateN

3.1.2

A bioinformatics tool for estimating population sizes and gene flow

MIRA

3.4.0, 3.9.18

A very efficient equence assembler

miRDeep2

0.0.5

Discovers microRNA genes by analyzing sequenced RNAs.

miRDP

1.3

miRDP can identify miRNA genes in plant species, ans assign expression status to individual genes.

MISO

0.4.7, 0.4.8, 0.4.9

Probabilistic analysis of RNA sequencing data for identifying isoform regulation.

MITEHunter

201111

Identify miniature inverted repeat transposable elements (MITEs) as well as other small (< 2Kb, default) class 2 nonautonomous transposable.

mlpy

3.5.0

 

MLTreemap

2.061

Functional Area: bioinformatics

mothur

1.18.0, 1.20.3, 1.21.1, 1.23.0, 1.23.1, 1.24.0, 1.24.1, 1.25.0, 1.26.0, 1.27.0, 1.29.0, 1.30.1, 1.31.2, 1.31.2b, 1.33.0, 1.33.0b, 1.33.2, 1.33.2b

A microbial ecology bioinformatics package

motility

0.8.2

A Python module for searching DNA for several different types of motif representations.

MPI-PHYLIP

20101115

An MPI redesigned version of PHYLIP - a computational package used for inferring phylogenies

mpi4py

1.3b

A Python module for reading and manipulating SAM files.

mpiBLAST

1.6.0

A parallel implementation of NCBI BLAST built for OpenMPI

MrBayes

3.2.1

Performs Bayesian inference and model choic across a wide range of phylogenetic and evolutionary models.

mreps

2.5

Used for identifying serial repeats (usually called tandem repeats) in DNA sequences.

MUMmer

3.22, 3.23

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.

MUMmerGPUpp

0.1

GPU version of MUMmer.

MUSCLE

3.8.31

Multiple sequence alignment.

ncbi

12.0.0, 7.0.0

Portable general purpose and biotech libraries.

networkx

1.1, 1.6, 1.9

 

newickUtils

1.6

A suite of shell tools to process phylogenetic trees.

NextClip

20140606

Nextera Long Mate Pair analysis and processing tool.

NGSUtils

0.5.0c

A suite of software tools for working with next-generation sequencing datasets.

nonpareil

2.2

Uses read redundancy in metagenomic data to estimate average coverage and predict the amount of sequences that will be required to achieve nearly complete coverage.

nseg

1.0

An ancient ncbi program needed by RepeatScout.

oases

0.1.22, 0.2.07, 0.2.08.BA

De novo transcriptome assembler for very short reads

OpenBUGS

3.2.1

BUGS is a software package for performing Bayesian inference Using Gibbs Sampling

orthomcl

1.4, 2.0.2

The deprecated/unsupported version of the OrthoMCL sequence assembler

PaCE

2.2

 

PAML

4.4e

Tools for performing phylogenetic analyses of DNA or protein sequences using maximum likelihood.

pandaseq

20130611

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence.

ParsInsert

1.04

Produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.

pbcore

20130508

A Python library for reading and writing PacBio® data files.

pbh5tools

20130508

A swiss-army knife for interrogating PacBio® HDF5 files (cmp.h5, bas.h5).

PBSuite

14.5.13, 14.6.24

PBJelly and PBHoney Pacbio finishing tools

PeakSeq

1.1

A program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

PfamScan

20101129

Searches protein fasta sequences against the Pfam library of HMMs.

PGDSpider

2.0.7.0

An automated data conversion tool for connecting population genetics and genomics programs.

PHAST

1.3

A package for comparative and evolutionary genomics.

phd2fasta

0.990622

Converts the phd files produced by phred and consed to fasta format.

phrap

0.990329, 1.090518

phrap is a program for assembling shotgun DNA sequence data

phred

020425, 071220

Reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

PHYLIP

3.5, 3.69

A computational package used for inferring phylogenies

PhyloSift

1.0.0.01

Phylogenetic analysis of genomes and metagenomes.

PhyML

3.0

For phylogenetic tree development.

phyutility

2.2.6

Phyutility (fyoo-til-i-te) is a command line program that performs simple analyses or modifications on both trees and data matrices.

picardTools

1.113, 1.89

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files.

PICRUSt

1.0.0

PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene surveys and full genomes.

PILER

1.0

A package for genomic repeat analysis

Pindel

20131030

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data.

plink

1.07

A whole genome association analysis toolset for the analysis of genotype/phenotype data.

polyphred

6.18

PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.

pplacer

1.1.alpha13r2

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

PRANK

111130

Multiple sequence alignment.

Primer3

2.3.4

PCR Primer Design Tool

PRINSEQ

0.19.5

.

PROBCONS

1.12

Multiple sequence alignment.

prodigal

2.60

Prokaryotic Gene Prediction Program

prokka

1.7

Prokka is an annotation pipeline for prokaryotic organisms.

PyCogent

1.5.1, 1.5.3

A Python module for probablistic techniques for working with biological sequences.

pyExcelerator

0.6.4.1

 

pyfasta

0.4.5

 

pygr

0.8.2

A Python package for sequence and comparative genomics analyses, even with extremely large multi-genome data sets.

Pylxml

2.3.5

 

PyML

0.7.11

 

PyMySQL

1.2.3

 

PyNAST

1.1, 1.2

A Python module for nearest alignment space termination tool.

pyqi

0.2.0, 0.3.2

 

PySAM

0.6

 

PythonCard

0.8.2

 

qcli

0.1.0

 

QIIME

1.4.0, 1.5.0, 1.6.0, 1.7.0

QIIME (pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).

QUAST

2.3

The tool evaluates genome assemblies by computing various metrics.

QuEST

2.4

Statistical software for analysis of ChIP-Seq data, including peak calling

Queue

2.7.4

Provides scatter-gather parallelization of GATK.

Randfold

2.0

Randfold

raxml

20120507, 7.2.6, 7.3.0, 7.7.8, 8.0.6

A fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments.

Ray

2.0.0

library for data formats

RDPClassifier

2.2, 2.6

A naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus, with confident estimates for each assignment.

RECON

1.05, 1.07, 1.08

A package for automated de novo identification of repeat families from genomic sequences

RepeatExplorer

0.9.7.7

Tool for solving repeats and scaffolds with Pacbio Data

RepeatMasker

3.3.0, 4.0.0, 4.0.5

Screens DNA sequences for interspersed repeats and low complexity DNA sequences.

RepeatModeler

1.0.5, 1.0.7, 1.0.8

A de-novo repeat family identification and modeling package.

RepeatScout

1.0.5

RepeatScout is a tool to discover repetitive substrings in DNA.

Rfam

1.0.4

.

riboPicker

0.4.3

Automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

RMBlast

1.2, 2.2.27, 2.2.28

RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.

RMTGeneNet

2.3

Pearson correlations for gene expression data and RMT thresholding of gene co-expression.

rnammer

1.2

RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.

RPy

2.3.0

 

RSEM

1.1.13, 1.1.20, 1.1.21, 1.2.0, 1.2.10, 1.2.11

A package for estimating gene and isoform expression levels from RNA-Seq data.

rtax

0.981, 0.983

Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene.

ruffus

2.2

Ruffus is a lightweight python module for running computational pipelines.

SAMStat

20130521

Displays various properties of next-generation sequencing reads stored in SAM/BAM format.

SAMTools

0.1.12a, 0.1.18, 0.1.19, 0.1.7a

Various utilities for manipulating SAM (Sequence Alignment/Map) format for storing large nucleotide sequence alignments

ScalaBLAST

2.4.53

Parallel Basic Local Alignment Search Tool

scanForMatches

20100914

Pattern scan software used by Biopieces

scikit

0.13.1

A set of python modules for machine learning and data mining.

screed

0.5, 08272012

screed is a database generation and querying package made to be used with gene sequences generated by Solexa machines, namely the FASTQ format, though FASTA is supported by default as well.

seg

19941018

SEG takes FASTA formatted files and filters them to remove redundancies and low complexity sequences. Output in various formats.

SeqClean

20130718

A script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.

seqtk

1.0

FASTA and FASTQ manipulation binaries

SGA

0.10.13

SGA is a memory efficient de novo genome assembler based on the concept of string graphs.

SHORE

0.9.0

Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform.

SHOREmap

2.1

SHOREmap is a software for mapping-by-sequencing, i.e., linking a genomoic region to a trait in plants through analyzing allele frequencies (AFs) in a pool of sequenced genomes or transcriptomes.

SHRIMP

2.2.3

 

sickle

1.210

A windowed adaptive trimming tool for FASTQ files using quality.

SIFT

1.03

.

SIFT_4G

1.0--Binary

Prediction of transmembrane helices in proteins.

signalp

4.1

Protein localization prediction

SIMCOAL2

2.1.2

A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models.

SLIDE

3.4

A computational screening and docking tool designed to find ligands with good steric and chemialcomplementarity

SLOPE

20140114

Finds the best split-read alignments to the reference genome, and clusters and outputs alignments.

SnpEff

3.3e

A variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants.

SOAP

1.11

Short Oligionucleotide Alignment Program

SOAP2

2.21

Short oligonucleotide alignment, redesigned version of Soap1 for large data sets.

SOAP3

r146

GPU version, short oligonucleotide alignment, redesigned version of Soap1 for large data sets.

SOAP3dp

1.4

GPU, dynamic programming version of short oligonucleotide alignment, redesigned version of Soap1 for large data sets.

SOAPcoverage

2.7.7

Calculates sequencing or physical coverage, duplication rate and block details for segments and whole genomes

SOAPdenovo

1.05

A novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads

SOAPdenovo2

r224, r240

A novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads

SOAPdenovoTrans

1.04

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.

SOAPindel

1.1, 2.1

Calls indels on paired-end sequencing data.

SOAPsnp

1.02

A resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference.

SOAPsv

1.02

A program for detecting the structural variation by whole genome de novo assembly System Requirements.

SomaticSniper

20140604

Identifies SNPs that are different between tumor and normal (or in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences.

SOPRA

1.4.6

Contig scaffolding assembler for mate pair/paired-end reads from Illumina and SOLiD platforms

SPAdes

3.0.0

Genome Assembler

SpliceGrapher

0.2.1

 

squidlib

1.9

Support for Randfold

SRAToolkit

2.1.16, 2.1.8, 2.3.2.4, 2.3.4.2

Loading and dumping tools for files retrieved from the NCBI Sequence Read Archive (SRA).

SSAHA2

2.5.5

Functional Area: Bioinformatics

SSAKE

3.8

Assembler for millions of very short DNA sequences

SSPACE

2.0

A standalone application for scaffolding pre-assembled contigs using paired-read data

stacks

0.998, 1.19

A software pipeline for building loci out of a set of short-read sequenced samples.

STAMP

2.0.0, 2.0.2

 

STAMPmotif

1.1

 

Stampy

1.0.23

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome.

STAR

2.3.0e

STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.

structure

2.3.4

Software For Inferring Population Structure.

SVDetect

0.8b

A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.

tabix

0.2.6

Generic indexer for TAB-delimited genome position files.

Tablet

1.12.03.26

Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.

TAMO

1.0

 

taxtastic

0.3.2

 

tbl2asn

20131114

Automates the submission of sequence records to GenBank.

tcoffee

9.01

A multiple sequence aligning package

TMHMM

2.0c

Prediction of transmembrane helices in proteins.

TopHat

1.2.0, 1.3.1, 1.4.1

A fast splice junction mapper for RNA-Seq reads.

TopHat2

2.0.0, 2.0.11, 2.0.4, 2.0.5, 2.0.8b, 2.0.12

A fast splice junction mapper for RNA-Seq reads.

TransABySS

1.3.2, 1.4.8

.

TransDecoder

20140116

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

transrate

0.2.0

Quality assessment and comparison of transcriptome assemblies.

trf

4.04

A program to locate and display tandem repeats in DNA sequences.

TrimGalore

0.3.3

A wrapper script that trims sequences by combining cutadapt and FastQC.

Trimmomatic

0.30, 0.32

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

trinity

20110820, 20111029, 20120608, 20121005, 20130108, 20130225, 20140413p1, 2.0.6, 2.1.1

A novel method for he efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.

tRNAscan-SE

1.3.1

Search for tRNA genes in genomic sequence.

UCHIME

4.2.40

Functional Area: Bioinformatics

uclust

1.2.15, 1.2.22q

Extreme high-speed sequence clustering, alignment and database search.

ucscUtils

262

Handy standalone command line tools for format conversions, searches, mapping transformations, etc, from UCSC.

ugene

1.11, 1.9.8

A multifaceted genome analysis suite.

USEARCH

5.2.236, 5.2.32, 6.0.152, 6.0.307, 6.1.544

High-throughput biological sequence analysis.

VarScan

2.3.6

Variant detection in massively parallel sequencing.

vcflib

20140522

A C++ library for parsing and manipulating VCF files.

vcftools

0.1.12a, 0.1.8a, 0.1.9

a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.

velvet

1.1.01, 1.1.05, 1.2.06, 1.2.07, 1.2.08.BA

Sequence assemble for very short reads.

velvet_st

1.2.08

Sequence assemble for very short reads.

Vienna

1.8.5

A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Vmatch

2.2.0, 2.2.2

Vmatch is a tool for solving large scale sequence matching tasks.

VMD

1.9.1

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

WebLogo

2.8.2

Application designed to generate sequence motif logos.

wgscelera

6.1, 7.0

A de novo whole-genome shotgun (WGS) DNA sequence assembler.

wise2

2.1.20c, 2.2.3rc7

Compares DNA sequences at level of its protein translation, to allow simultaneous prediction of say gene structure with homology based alignments.


 

 

Biology Software

Module Name

Version

Brief Description

SEEDS

1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6, 1.0.7, 1.0.8, 1.0.9, 1.0.10, 1.0.11, 1.0.12, 1.0.13

Stochastic Cellular Artificial Life Simulator

avida

2011.09.05

Program for studying biological evolution.

NetworkX

1.1,1.6,1.9

Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Chemistry Software

Module Name

Version

Brief Description

Amber

11, 12, 12-cuda, 14, 14-cuda, 14-tools

Assisted Model Building with Energy Refinement

bachelor

20110518

Some home grown code that converts 3x3 rotational matrices to XYZ Euler angles.

DOCK

6.5

Software to predict binding of modes on a molecule

GAMESS

20110811, 20110811r1, 20120501r1

General Atomic and Molecular Electronic Structure System - a general ab initio quantum chemistry package

Gaussian

g09-legacy

It provides state-of-the-art capabilities for electronic structure modeling

Molpro

2010.1

Molpro is a complete system of ab initio programs for molecular electronic structure calculations

nbo

6

Through their close association with elementary Lewis structure diagrams, NBOs provide a direct link to familiar valency and bonding concepts. Unlike delocalized MOs (whose sprawling forms vary bewilderingly even between closely related systems), NBOs are highly conserved and transferable from one

NWChem

6.0, 6.3

NWChem is a computational chemistry software package.

VASP

5.2.12, 5.3

the Vienna Ab initio Simulation Package .

Engineering Software

Module Name

Version

Brief Description

Abaqus

6.11-2

 

ANSYS

14.0, 14.5.7, 15.0.7, 16.0

 

Fire Dynamics Simulator (FDS)

5.5.3, 6.0.11

Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.

GAMBIT

2.4.6

 

HEEDS

6.0, 7.0, 7.2

 

HFSS

14.0, 15.0

 

OpenFOAM

2.1.1, 20140710_2.3.x

Open Source CFD Solver.

Tecplot360

13.3, 14.0, 2013R1

 

xoopic

2.70

particle in cell code

Geography Software

Module Name

Version

Brief Description

GDAL

1.10.1, 1.8.1, 1.9.2

A geospatial data abstraction library

GDL

0.9.2

GNU Data Language.

GRASS

6.4.3RC2, 6.4.3RC3

The GRASS (Geographic Resources Analysis Support System).

HDF5

1.8.10, 1.8.7

HDF5: parallel (fortran) and serial (c) Libraries and data constructs for managing data.

NCL

6.0.0, 6.1.2

NCAR's Command Languages.

PROJ.4

4.7.0, 4.8.0

Cartographic Projections Library.

Mathematics Software and Libraries

Module Name

Version

Brief Description

ACML

5.0.0

AMD Core Math Library

ADMB

11.1, 20121219

The AD Model Builder - a powerful software package for the development of state-of-the-art nonlinear statistical models.

ALPS

2.1.1-r6176

The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.

arpack-ng

3.1.2

Libraries for solving large scale eigenvalue problems

ATLAS

3.8.4, 3.10.2

PETSc is a collection of libraries and data structures for large scale scientific computing.

bcbb

20130430

 

bioscriptsConvert

0.4

Biopython scripts for converting molecular sequences between formats.

BLAS

20110922

Parallel Visualization Program.

bxPython

2.7

A Python module for manipulating multiple sequence alignments.

cairo

1.12.16

 

clapack

3.2.1

blas library with c-bindings

CUnit

2.1.2

Automated testing framework for 'C'.

Cusp

0.2.0

generic parallel algorithms for sparse matrix graph computations on GPGPUS.

cutadapt

1.1, 1.2.1, 1.4.1

 

dateutil

1.5

A Python module extension for date time functions.

DendroPy

3.12.0

 

dislin

10.3

Dislin is a scientific plotting library.

docutils

0.11

 

Eigen

3.0.3

C++ templates for linear algebra.

emperor

0.9.1

 

ETE2

2.2.r1019

 

ete2

2.1.539

 

expat

2.0.1

XML parser library.

FastCGI

2.4.0

FastCGI - CGI for distributed Computing?

fftw

2.1.5, 3.3, 3.3.3

Libraries for performing fast fourier transforms.

fisher

0.1.4

 

GAMS

24.1

General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers. GAMS is tailored for complex, large scale modeling applications, and allows you to build large maintainable models that can be adapted quickly to new situations.

GAUSS

gauss12.1

GAUSS is statistical software

gdata

20131104

 

GEOS

3.3.8

C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions.

GeoTIFF

1.2.5

Libegeotiff is an open source library for reading and writing GeoTIFF information tgs.

GLEW

1.9.0

The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library.

glib

2.35.9

 

GMP

5.0.2, 5.1.3

GNU Multiple Precision Arithmetic Library.

gsl

1.15, 1.16

The GNU Scientific Library - numerical lib for C and C++ programmers.

guile

2.0.5.12-8d154, 20120203

GNU Extension Language.

h5py

2.1.3

The h5py package is a Pythonic interface to the HDF5 binary data format.

HDF

4.2.7

HDF: Libraries and data constructs for managing data.

HDF5

1.8.10, 1.8.7

HDF5: parallel (fortran) and serial (c) Libraries and data constructs for managing data.

HDF5-C

1.8.10-patch1

HDF5: Libraries and data constructs for managing data.

IlmBase

1.0.2

Libraries and headers for encapsulatin our 16-bit floating point format, a thread abstraction library for use with OpenEXR, vector library, exception handling library.

LAPACK

3.3.1, 3.4.2, 3.4.2b

Linear Algebra Library.

libmatheval

1.1.8

libmatheval – a library to parse and evaluate symbolic expressions.

libmpeg2

0.5.1

a free MPEG-2 video stream decoder

libunwind

1.0.1

A portable C API to determine the call-chain of a program. Used by google perftools.

LLVM

2.9, 3.0

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.

lxml

3.2.3

 

magma

1.4.0-Kepler, 1.4.0-Tesla

cuda enabled lapack libraries

Mathematica

8.0, 9.0.1

Mathematica

MATLAB

R2011a, R2011b, R2012a, R2012b, R2013a, R2013b, R2014a

This module loads libraries need to compile, and run compiled MATLAB code without licenses.

matplotlib

1.1.0, 1.1.0a, 1.2.1, 1.3.1

A useful plotting package for Python

Mesa

7.11

The Mesa 3D Graphics Library (OSMesa)

METIS

5.0.2, 5.1.0

graph partioning library

MISO

0.4.7, 0.4.8, 0.4.9

Probabilistic analysis of RNA sequencing data for identifying isoform regulation.

MKL

10.3, 11.0, 11.1

 

mlpy

3.5.0

 

motility

0.8.2

A Python module for searching DNA for several different types of motif representations.

MPFR

3.1.2

GNU Multiple Precision Floating Point Library.

mpi4py

1.3b

A Python module for reading and manipulating SAM files.

MySQLdb

1.2.4

 

networkx

1.1, 1.6, 1.9

 

NumPy

1.5.0, 1.5.1, 1.6.1, 1.8.0, 1.8.1, 1.6.1c

 

Octave

3.4.3

octave – an opensource scientifici computing platform, similar to MATLAB.

ODE

0.12

Open Dynamics Engine: a hpc library for simulating rigid body dynamics.

OpenCV

2.4.0

library of programming functions for real time computer vision

OpenEXR

1.7.0

Library for storing 16-bit FP images using the EXR format

openjpeg

20121215

JPEG 2000 codec

openpyxl

1.6.1

 

pbcore

20130508

A Python library for reading and writing PacBio® data files.

pbh5tools

20130508

A swiss-army knife for interrogating PacBio® HDF5 files (cmp.h5, bas.h5).

perftools

1.8.3

A fast multi-threaded malloc and performance analysis tool. Used by MIRA.

PETSc

3.2-p2, 3.3-p4, 3.4.2

PETSc is a collection of libraries and data structures for large scale scientific computing.

pHDF5

1.8.10-patch1

HDF5: Libraries and data constructs for managing data (fortran).

PIL

1.1.7

 

PLplot

5.0.1, 5.9.9

Cross-platform software package for creating scientific plots

PROJ.4

4.7.0, 4.8.0

Cartographic Projections Library.

pyamg

2.0.0

 

pycairo

1.12.16

 

PyCogent

1.5.1, 1.5.3

A Python module for probablistic techniques for working with biological sequences.

PyCUDA

2011.1.2, 2013.1.1

 

pyExcelerator

0.6.4.1

 

pyfasta

0.4.5

 

PyGLPK

0.3

Specify linear programs (LPs) and mixed integer programs (MIPs), and to solve them with either simplex, interior-point, or branch-and-bound algorithms

Pylxml

2.3.5

 

PyML

0.7.11

 

PyMySQL

1.2.3

 

PyNAST

1.1, 1.2

A Python module for nearest alignment space termination tool.

PyParsing

2.0.1

A general parsing module for Python.

pyqi

0.2.0, 0.3.2

 

PyQt

4.9.4

 

PySAM

0.6

 

PythonCard

0.8.2

 

qcli

0.1.0

 

Qhull

2011.2, 2012.1

Math library to compute conve hulls, Delaunay triangulation, Voronoi diagrams.

qrupdate

1.1.1, 1.1.2

Libraries for performing .

R

2.12.0, 2.13.0, 2.13.2, 2.14.1, 2.15.1, 2.15.1b, 3.0.1, 3.1.0, 2.15.2

R is an advanced statistical analysis and plotting program.

RPy

2.3.0

 

ruffus

2.2

Ruffus is a lightweight python module for running computational pipelines.

SAS

9.3, 9.3m2

SAS is data analysis and statistical software

scikit

0.13.1

A set of python modules for machine learning and data mining.

SciPy

0.11.0, 0.12.0, 0.13.0, 0.13.3, 0.9.0, 0.9.0b

 

scons

2.1.0

SCons is a software construction tool (build tool, substitute for Make) implemented in Python.

silo

4.9.1

meshing / field i/o library and database

simplejson

3.1.2

 

SIP

4.13.3

Python bindings for C/C++ libraries.

SLEPc

3.3-p3

SLEPC: Scalable Library for Eigen Value Problem Computations.

SOAPpy

0.11.6

Web services for Python.

sparsehash

1.11, 2.0.2

Library for extremely optimized hash tables.

Stata

12.0, 13.0

Stata is a data analysis and statistical software

SuiteSparse

3.6.1, 3.7.0, 4.2.1

Suite of programs dealing with sparse matrices.

SymPy

0.7.5

 

szip

2.1

Compression library.

TAMO

1.0

 

taxtastic

0.3.2

 

thrust

1.4.0

Data structures for matrix algebra.

tweetstream

1.1.1

A Python API module for Twitter streaming.

wxPython

2.8.12.1

 

wxWidgets

2.8.12

Cross platform GUI library

xlrd

0.8.0

 

zlib

1.2.7

Compression library.

Molecular Dynamics Software

Module Name

Version

Brief Description

espresso

5.0.3-svn-10833

Quantum Espresso:computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

GROMACS

4.0.7, 4.5.5

Molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids.

LAMMPS

20111219, 20120111, 20130129, 20130129b, 20131029

LAMMPS Molecular Dynamics Simulator

NAMD

2.8, 2.9

A Scalable molecular dynamics code based on charm++.

OpenMM

3.1.1

Library which provides tools for modern molecular modeling simulation.

Python-ase

3.8.1

atomic simulation environment

SIESTA

3.1

Spanish Initiative for Electronic Simulation with Thousands of Atoms

TranSiesta

3.1.p424

Spanish Initiative for Electronic Simulation with Thousands of Atoms (With TranSiesta Module)

Profiling and Debugging Tools

Module Name

Version

Brief Description

allinea

4.2-34404, 4.2-pr, 5.0.1-42607

 

cube

3.3.2

CUBE is a presentation component suitable for displaying a wide variety of performance and correctness data for parallel programs including MPI and OpenMP applications. CUBE allows interactive exploration of the performance data in a scalable fashion

MPICH

1.2.7

PGI's build of MPICH MPI implementation with Infiniband support.

MVAPICH

1.1

A variant of the popular MPICH MPI implementation with Infiniband support.

MVAPICH2

1.7-r5078, 1.8-a1p1, 2.0a, 1.8-r5423, 1.9a2, 2.0rc1, 1.9rc1

A variant of the popular MPICH MPI implementation with Infiniband support.

ompP

0.8.3

OMP Profiler.

perftools

1.8.3

A fast multi-threaded malloc and performance analysis tool. Used by MIRA.

Scalasca

1.4.2

Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior.

TAU

2.22-p1, 2.21.2

profiling library

TotalView

8.12.0-1, 8.9.2-1

 

Valgrind

3.7.0

Profiler.

Programming

Module Name

Version

Brief Description

astyle

2.05.1

automatic formatter for C, C+, C+/CLI, Objective-C, C#, and Java source code

allinea

4.2-34404, 4.2-pr, 5.0.1-42607

 

boost

1.42.0, 1.47.0, 1.52.0, 1.55.0, 1.58.0

Boost is a C++ template library which provides a wide variety of useful functionality.

CERN ROOT

5.24

a modular scientific software framework.

Clang

20131226, 20140106

clang: a C language family frontend for LLVM

cudasdk

4.0, 4.2

Common Unified Device Architecture (CUDA) SDK for nVidia GPGPU platforms.

cudatoolkit

4.0, 4.2, 5.0, 5.5, 6.0

Common Unified Device Architecture (CUDA) toolkit for nVidia GPGPU platforms.

dmd

2.0606

D is a language with C-like syntax and static typing.

FastCGI

2.4.0

FastCGI - CGI for distributed Computing?

g95 Compiler

0.93

 

GCC

4.4.5, 4.7.1, 4.8.2, 4.8.3

 

GLEW

1.9.0

The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library.

GLPK

4.47, 4.54

GNU LInear Programming Kit.

GNU Toolchain

4.4.5

 

gparallel

20131022

A shell tool for executing jobs in parallel.

guile

2.0.5.12-8d154, 20120203

GNU Extension Language.

HPCToolkit

5.0.1

 

IMPI

4.0.1.007, cc4.1.0_libc2.4_kernel2.6.16.21, 4.1.0.024

An MPI implementation provided by Intel.

Intel Toolchain

2011.0, 2012.0, 2013.1, 2013.2, 2013sp1

 

Julia

0.4.1

High Level Programming language

Lua

5.2.0

Lua.

MATLAB

R2011a, R2011b, R2012a, R2012b, R2013a, R2013b, R2014a

This module loads libraries need to compile, and run compiled MATLAB code without licenses.

Mono

2.10.8

Cross platform development framework.

MPICH

1.2.7

PGI's build of MPICH MPI implementation with Infiniband support.

MPICH2

1.4.1p1

MPICH2 is an implementation of the Message Passing Interface (MPI).

MVAPICH

1.1

A variant of the popular MPICH MPI implementation with Infiniband support.

MVAPICH2

1.7-r5078, 1.8-a1p1, 2.0a, 1.8-r5423, 1.9a2, 2.0rc1, 1.9rc1

A variant of the popular MPICH MPI implementation with Infiniband support.

OCaml

3.12.1p

Compiler/interpreter for Caml.

OpenMPI

1.4.3, 1.4.3b, 1.4.4, 1.5.3, 1.6.3, 1.6.4, 1.6.5, 1.7.3, 1.8, 1.8.1

OpenMPI is a popular implementation of the Message Passing Interface (MPI)

pascal

2.4.4

Free Pascal compiler.

PGI Toolchain

11.10, 12.3, 12.4, 13.10, 13.4, 14.1, 14.6

 

Python

2.6.7, 2.7.2, 3.2.1, 3.3.2

Python is a powerful programming language used for a wide variety of tasks.

ruby

1.9.3, 2.1.2

Ruby programming language.

swig

2.0.11

interface compiler that conncts programs written in c and c++ with scripting languages such as perl, python, ruby and tcl.

TBB

4.1.1.117

 

TotalView

8.12.0-1, 8.9.2-1

 

UDUNITS

2.1.24

utilies for processing netcdf files

ufl

20131126

unified form language.

Python related modules

Module Name

Version

Brief Description

bcbb

20130430

 

biomformat

0.9.3, 1.2.0, 1.3.0

A Python module for comparative genomics.

Biopython

1.58, 1.61, 1.65

a set of freely available tools for biological computation.

bioscriptsConvert

0.4

Biopython scripts for converting molecular sequences between formats.

bxPython

2.7

A Python module for manipulating multiple sequence alignments.

cutadapt

1.1, 1.2.1, 1.4.1

 

dateutil

1.5

A Python module extension for date time functions.

DendroPy

3.12.0

 

docutils

0.11

 

emperor

0.9.1

 

ETE2

2.2.r1019

 

ete2

2.1.539

 

fisher

0.1.4

 

gdata

20131104

 

h5py

2.1.3

The h5py package is a Pythonic interface to the HDF5 binary data format.

lxml

3.2.3

 

matplotlib

1.1.0, 1.1.0a, 1.2.1, 1.3.1

A useful plotting package for Python

MISO

0.4.7, 0.4.8, 0.4.9

Probabilistic analysis of RNA sequencing data for identifying isoform regulation.

mlpy

3.5.0

 

motility

0.8.2

A Python module for searching DNA for several different types of motif representations.

mpi4py

1.3b

A Python module for reading and manipulating SAM files.

MySQLdb

1.2.4

 

networkx

1.1, 1.6, 1.9

 

NumPy

1.5.0, 1.5.1, 1.6.1, 1.8.0, 1.8.1, 1.6.1c

 

openpyxl

1.6.1

 

pbcore

20130508

A Python library for reading and writing PacBio® data files.

pbh5tools

20130508

A swiss-army knife for interrogating PacBio® HDF5 files (cmp.h5, bas.h5).

PIL

1.1.7

 

pyamg

2.0.0

 

pycairo

1.12.16

 

PyCogent

1.5.1, 1.5.3

A Python module for probablistic techniques for working with biological sequences.

PyCUDA

2011.1.2, 2013.1.1

 

pyExcelerator

0.6.4.1

 

pyfasta

0.4.5

 

PyGLPK

0.3

Specify linear programs (LPs) and mixed integer programs (MIPs), and to solve them with either simplex, interior-point, or branch-and-bound algorithms

Pylxml

2.3.5

 

PyML

0.7.11

 

PyMySQL

1.2.3

 

PyNAST

1.1, 1.2

A Python module for nearest alignment space termination tool.

PyParsing

2.0.1

A general parsing module for Python.

pyqi

0.2.0, 0.3.2

 

PyQt

4.9.4

 

PySAM

0.6

 

Python

2.6.7, 2.7.2, 3.2.1, 3.3.2

Python is a powerful programming language used for a wide variety of tasks.

Python-ase

3.8.1

atomic simulation environment

PythonCard

0.8.2

 

qcli

0.1.0

 

QUAST

2.3

The tool evaluates genome assemblies by computing various metrics.

RPy

2.3.0

 

ruffus

2.2

Ruffus is a lightweight python module for running computational pipelines.

scikit

0.13.1

A set of python modules for machine learning and data mining.

SciPy

0.11.0, 0.12.0, 0.13.0, 0.13.3, 0.9.0, 0.9.0b

 

scons

2.1.0

SCons is a software construction tool (build tool, substitute for Make) implemented in Python.

simplejson

3.1.2

 

SIP

4.13.3

Python bindings for C/C++ libraries.

SOAPpy

0.11.6

Web services for Python.

SymPy

0.7.5

 

TAMO

1.0

 

taxtastic

0.3.2

 

tweetstream

1.1.1

A Python API module for Twitter streaming.

Valgrind

3.7.0

Profiler.

wxPython

2.8.12.1

 

xlrd

0.8.0

 

Utilities

Module Name

Version

Brief Description

AGREP

3.41

 

autoconf

2.69

a package for generating configure scripts

automake

1.15

a tool for automatically generating Makefile.in files

BLACS

1.1.03

communication library for BLAS

cctools

3.4.1

The cctools package contains Parrot, Chirp, Makeflow, Work Queue, SAND, and other software.

cmake

2.8.10.2, 2.8.5, 2.8.7, 2.8.8, 3.0.0

CMake is a popular system for the configuration, compilation, and installation of software.

condor

7.6.4-1

 

Devolab dist_run Tools

1.0

Functional Area: Utilities

Eigensoft

3.0, 4.2

Using Principal component analysis to model ancestry differences

espresso-ab

1.0

espresso-ab – converts Boolean logic espressions into a truth table

expat

2.0.1

XML parser library.

FFmpeg

1.2, 35817, 35817b

FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards committee, the community or a corporation. It contains libavcodec, libavutil, libavformat, libavdevice, libswscale and libswresample which can be used by applications. As well as ffmpeg, ffserver, ffplay and ffprobe which can be used by end users for transcoding, streaming and playing

FLTK

1.3.0, 1.3.2

Fast Light Toolkit (c++ gui).

git

1.7.11.5

revision control software

gperf

3.0.4

hash generator

GraphicsMagick

1.3.13, 1.3.15, 1.3.17

Image processing Library.

gt

5.2.0

Globus Toolkit for grid computing

Hadoop

1.0.1, 2.4.1

 

HDF5

1.8.10, 1.8.7

HDF5: parallel (fortran) and serial (c) Libraries and data constructs for managing data.

IlmBase

1.0.2

Libraries and headers for encapsulatin our 16-bit floating point format, a thread abstraction library for use with OpenEXR, vector library, exception handling library.

ImageJ

1.46r

 

Java

1.6.0_31, 1.7.0_51

Java Runtime Environment

LLVM

2.9, 3.0

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.

Mesa

7.11

The Mesa 3D Graphics Library (OSMesa)

METIS

5.0.2, 5.1.0

graph partioning library

MPlayer

20120130

Video Encoder.

MyHadoop

2.2.0

 

netCDF

3.6.3, 4.1.3

library for data formats

NetworkX

1.6

Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

Newbler

2.9

Newbler Assembly Tools

openpyxl

1.6.1

 

ORCA

2360

 

ParMETIS

4.0.2

parallel graph partioning library

perl

5.18.2

A more bleeding edge version of the Perl interpreter.

PROJ.4

4.7.0, 4.8.0

Cartographic Projections Library.

Pylxml

2.3.5

 

PyMySQL

1.2.3

 

Qt

4.7.4

Widget Toolkit.

rdesktop

1.7.0, 1.7.1

remote desktop

scons

2.1.0

SCons is a software construction tool (build tool, substitute for Make) implemented in Python.

SnapRestore

3.0

Tool to restore from ZFS Snapshots

Sowing

1.1.16

Sowing is a collection of documentation and API generator tools.

sparsehash

1.11, 2.0.2

Library for extremely optimized hash tables.

szip

2.1

Compression library.

tbl2asn

20131114

Automates the submission of sequence records to GenBank.

unrar

0.0.1, 4.2.4

 

Weka

3-6-9

 

XZUtils

5.0.5

A general-purpose data compressions package with high compression ratio.

zlib

1.2.7

Compression library.

Visualization

Module Name

Version

Brief Description

AFINI

2014, 2011

software for the analysis and display of fMRI data.

batik

1.7

used to render, generate, and manipulate SVG graphics

Blender

2.59

an open-source application designed to visualize large (and small) datasets.

CASA

4.5.0

the Common Astronomy Software Applications package

FFmpeg

1.2, 35817, 35817b

FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards committee, the community or a corporation. It contains libavcodec, libavutil, libavformat, libavdevice, libswscale and libswresample which can be used by applications. As well as ffmpeg, ffserver, ffplay and ffprobe which can be used by end users for transcoding, streaming and playing

FreeSurfer

5.1.0, 5.3.0

FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

gnuplot

4.4.4, 4.6.3, 4.6.1

gnuplot: an opensource, command line driven graphing utility.

ImageMagick

6.7.2-3

an open-source application designed to visualize large (and small) datasets.

JasPer

1.900.1

open source jpeg codec

matplotlib

1.1.0, 1.1.0a, 1.2.1, 1.3.1

A useful plotting package for Python

MPlayer

20120130

Video Encoder.

OpenCV

2.4.0

library of programming functions for real time computer vision

OpenEXR

1.7.0

Library for storing 16-bit FP images using the EXR format

openjpeg

20121215

JPEG 2000 codec

ParaView

3.10.1, 3.14.1, 4.0.1

Parallel Visualization Program.

PIL

1.1.7

 

PyQt

4.9.4

 

R

2.12.0, 2.13.0, 2.13.2, 2.14.1, 2.15.1, 2.15.1b, 3.0.1, 3.1.0, 2.15.2

R is an advanced statistical analysis and plotting program.

SAS

9.3, 9.3m2

SAS is data analysis and statistical software

Stata

12.0, 13.0

Stata is a data analysis and statistical software

Tecplot360

13.3, 14.0, 2013R1

 

VAPOR

2.1.0

A Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers.

VTK

6.1.0

Visualization ToolKit

wxWidgets

2.8.12

Cross platform GUI library

xgrafix

2.70.4

graphical companion to xoopic

XMakemol

5.16

Program for viewing and manipulating atomic and other chemical properties.

Software Specific Tutorials

Various software specific tutorials are available .

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