Difference between revisions of "Biocluster Applications"

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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!Application
 
!Application
 
!Installed Versions
 
!Installed Versions
 +
|-
 +
|
 +
|, , , , , , , , , , , , , , , , , , , , ,
 +
|
 +
|
 
|-
 
|-
 
|454
 
|454
 
|2.6, 2.7, 2.8
 
|2.6, 2.7, 2.8
 +
|
 +
|adds environmental variables to 454
 
|-
 
|-
 
|AbundantOTU+
 
|AbundantOTU+
 
|0.91b
 
|0.91b
 +
|
 +
|adds environmental variables to AbundantOTU+
 
|-
 
|-
 
|abyss
 
|abyss
 
|1.2.5, 1.3.3, 1.3.4
 
|1.2.5, 1.3.3, 1.3.4
 +
|
 +
|adds environmental variables to ABySS
 
|-
 
|-
 
|afni
 
|afni
 
|2011_12_21_2014
 
|2011_12_21_2014
 +
|
 +
|adds environmental variables to afni
 
|-
 
|-
 
|allpathslg
 
|allpathslg
 
|42911
 
|42911
 +
|
 +
|adds environmental variables for allpathslg
 
|-
 
|-
 
|amos
 
|amos
 
|3.1.0
 
|3.1.0
 +
|http://sourceforge.net/apps/mediawiki/amos
 +
|The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler.
 
|-
 
|-
 
|AmpliconNoise
 
|AmpliconNoise
 
|1.2.7
 
|1.2.7
 +
|
 +
|adds environmental variables to AmpliconNoise
 
|-
 
|-
 
|art
 
|art
 
|20110922
 
|20110922
 +
|
 +
|adds environmental variables to afni
 
|-
 
|-
 
|artemis
 
|artemis
 
|14.0
 
|14.0
 +
|
 +
|adds environmental variables to artemis
 
|-
 
|-
 
|augustus
 
|augustus
 
|2.6.1
 
|2.6.1
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
|
 +
|AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
 
|-
 
|-
 
|b2g4pipe
 
|b2g4pipe
 
|2.5
 
|2.5
 +
|
 +
|adds environmental variables to blast2go pipe
 
|-
 
|-
 
|babraham
 
|babraham
 
|bioinformatics
 
|bioinformatics
 +
|
 +
|Description of the module
 
|-
 
|-
 
|bali-phy
 
|bali-phy
 
|2.1.1
 
|2.1.1
 +
|
 +
|adds environmental variables to bali-phy
 
|-
 
|-
 
|bam2fastq
 
|bam2fastq
 
|1.1.0
 
|1.1.0
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|bamtools
 
|bamtools
 
|0.9.0
 
|0.9.0
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|bcbio-nextgen
 
|bcbio-nextgen
 
|0.6.5
 
|0.6.5
 +
|
 +
|A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. Homepage - https://bcbio-nextgen.readthedocs.org
 
|-
 
|-
 
|bedtools
 
|bedtools
 
|2.10.0, 2.10.1, 2.17.0
 
|2.10.0, 2.10.1, 2.17.0
 +
|
 +
|adds environmental variables to bedtools
 
|-
 
|-
 
|biodatabase
 
|biodatabase
 
|1.0
 
|1.0
 +
|
 +
|adds environmental variables to biodatabase scripts
 
|-
 
|-
 
|biopieces
 
|biopieces
 
|0.48
 
|0.48
 +
|
 +
|adds environmental variables, software, and bins to biopieces
 
|-
 
|-
 
|blast+
 
|blast+
 
|2.2.25+, 2.2.28+
 
|2.2.25+, 2.2.28+
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|blast-intel
 
|blast-intel
 
|2.2.26
 
|2.2.26
 +
|http://blast.ncbi.nlm.nih.gov/Blast.cgi
 +
|The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
 
|-
 
|-
 
|blast
 
|blast
 
|2.2.25, 2.2.26
 
|2.2.25, 2.2.26
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|blast2go
 
|blast2go
 
|2.5
 
|2.5
 +
|
 +
|Description of the module
 
|-
 
|-
 
|blat
 
|blat
 
|0.34
 
|0.34
 +
|
 +
|adds environmental variables to blat
 
|-
 
|-
 
|boost-intel
 
|boost-intel
 
|1.54
 
|1.54
 +
|http://www.boost.org/
 +
|Boost provides free peer-reviewed portable C++ source libraries.
 
|-
 
|-
 
|boost
 
|boost
 
|1.54
 
|1.54
 +
|http://www.boost.org/
 +
|Boost provides free peer-reviewed portable C++ source libraries.
 
|-
 
|-
 
|bowtie
 
|bowtie
 
|0.12.8, 0.12.9, 1.0.0
 
|0.12.8, 0.12.9, 1.0.0
 +
|http://bowtie-bio.sourceforge.net
 +
|Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
 
|-
 
|-
 
|bowtie2
 
|bowtie2
 
|2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0
 
|2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0
 +
|
 +
|adds environmental variables to Bowtie2
 
|-
 
|-
 
|breseq
 
|breseq
 
|0.24
 
|0.24
 +
|
 +
|{Determine mutations in evolved microbes from next-generation sequencing data. http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing
 
|-
 
|-
 
|bwa
 
|bwa
 
|0.5.9, 0.7.5a
 
|0.5.9, 0.7.5a
 +
|
 +
|bio-bwa.sourceforge.net BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome
 
|-
 
|-
 
|cafe
 
|cafe
 
|2.2, 3.0
 
|2.2, 3.0
 +
|
 +
|adds environmental variables to cafe
 
|-
 
|-
 
|casava
 
|casava
 
|1.8.2
 
|1.8.2
 +
|
 +
|adds environmental variables to casava
 
|-
 
|-
 
|cd-hit
 
|cd-hit
 
|4.6, 4.6.1
 
|4.6, 4.6.1
 +
|
 +
|CD-HIT Suite  http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide
 
|-
 
|-
 
|cdbfasta
 
|cdbfasta
 
|0.99
 
|0.99
−
|-
+
|http://cdbfasta.sourceforge.net/
−
|cegma
+
|fast indexing and retrieval of fasta records from flat file databases.
−
|v2.4.010312
 
 
|-
 
|-
 
|chance
 
|chance
 
|1.0
 
|1.0
 +
|
 +
|CHANCE - CHip-seq ANalytics and Confidence Estimation. songlab.ucsf.edu/Software.html
 
|-
 
|-
 
|chimera
 
|chimera
 
|1.5.3, 1.6.2
 
|1.5.3, 1.6.2
 +
|
 +
|adds environmental variables for chimera
 
|-
 
|-
 
|cisgenome
 
|cisgenome
 
|2.0
 
|2.0
 +
|http://www.biostat.jhsph.edu/~hji/cisgenome/
 +
|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
 
|-
 
|-
 
|ClonalFrame
 
|ClonalFrame
 
|1.2
 
|1.2
 +
|
 +
|adds environmental variables to ClonalFrame
 
|-
 
|-
 
|clustalo
 
|clustalo
 
|1.2.0
 
|1.2.0
 +
|
 +
|Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. clustal.org/omega
 
|-
 
|-
 
|clustalw
 
|clustalw
 
|2.1
 
|2.1
 +
|
 +
|adds environmental variables to clustalw
 
|-
 
|-
 
|cufflinks
 
|cufflinks
 
|1.1.0, 1.3.0, 2.0.2, 2.1.1
 
|1.1.0, 1.3.0, 2.0.2, 2.1.1
 +
|
 +
|adds environmental variables to cufflinks
 
|-
 
|-
 
|cutadapt
 
|cutadapt
 
|1.2
 
|1.2
 +
|
 +
|https://code.google.com/p/cutadapt/ cutadapt removes adapter sequences from high-throughput sequencing data.
 
|-
 
|-
 
|cytoscape
 
|cytoscape
 
|2.8.1, 2.8.3
 
|2.8.1, 2.8.3
 +
|
 +
|adds environmental variables to cytoscape
 
|-
 
|-
 
|EagleView
 
|EagleView
 
|2.2
 
|2.2
 +
|
 +
|adds environmental variables to EagleView
 
|-
 
|-
 
|efiest
 
|efiest
 
|alpha, devel
 
|alpha, devel
 +
|
 +
|adds environmental variables for EFI QUEST development branch
 
|-
 
|-
 
|EMBOSS
 
|EMBOSS
 
|6.5.7
 
|6.5.7
 +
|
 +
|adds environmental variables to EMBOSS
 
|-
 
|-
 
|erange
 
|erange
 
|3.2.1
 
|3.2.1
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|estscan
 
|estscan
 
|3.0.3
 
|3.0.3
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|fasta
 
|fasta
 
|36.3.5d
 
|36.3.5d
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|fasta_splitter
 
|fasta_splitter
 
|1
 
|1
 +
|
 +
|Description of the module
 
|-
 
|-
 
|fastqc
 
|fastqc
 
|0.10.1
 
|0.10.1
 +
|
 +
|adds environmental variables to fastqc
 
|-
 
|-
 
|fastsimcoal2
 
|fastsimcoal2
 
|1.1.1
 
|1.1.1
 +
|http://cmpg.unibe.ch/software/fastsimcoal2/
 +
|fast sequential Markov coalescent simulation of genomic data under complex evolutionary models.
 
|-
 
|-
 
|fasttree
 
|fasttree
 
|2.1.7
 
|2.1.7
 +
|
 +
|http://www.microbesonline.org/fasttree/ Infers ML phylogenetic trees from alignments
 
|-
 
|-
 
|fastx_toolkit
 
|fastx_toolkit
 
|0.0.13
 
|0.0.13
 +
|
 +
|adds environmental variables to fastx_toolkit
 
|-
 
|-
 
|findpeaks
 
|findpeaks
 
|3.1.9.2
 
|3.1.9.2
 +
|
 +
|adds environmental variables to findpeaks
 
|-
 
|-
 
|freebayes
 
|freebayes
 
|0.9.6
 
|0.9.6
 +
|
 +
|adds environmental variables to freebayes
 
|-
 
|-
 
|gatk
 
|gatk
 
|1.6-5, 1.6-13, 2.5-2, 2.6-4
 
|1.6-5, 1.6-13, 2.5-2, 2.6-4
 +
|http://www.broadinstitute.org/gatk
 +
|The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
 
|-
 
|-
 
|gcc
 
|gcc
 
|4.8.1
 
|4.8.1
 +
|
 +
|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system. The GNU system was developed to be 100% free software, free in the sense that it respects the user's freedom. Homepage : http://gcc.gnu.org
 
|-
 
|-
 
|geneid
 
|geneid
 
|1.0
 
|1.0
 +
|
 +
|adds environmental variables to geneid
 
|-
 
|-
 
|genomer
 
|genomer
 
|0.0.10
 
|0.0.10
 +
|
 +
|adds environmental variables to usearch
 
|-
 
|-
 
|genometools
 
|genometools
 
|1.5.1
 
|1.5.1
 +
|http://genometools.org/
 +
|The GenomeTools genome analysis system is a free 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.
 
|-
 
|-
 
|gff
 
|gff
 
|2.1
 
|2.1
 +
|
 +
|Description of the module
 
|-
 
|-
 
|glimmer
 
|glimmer
 
|3.02
 
|3.02
 +
|
 +
|adds environmental variables to bedtools
 
|-
 
|-
 
|gmap
 
|gmap
 
|2011-09-14, 2013-03-31
 
|2011-09-14, 2013-03-31
 +
|
 +
|adds environmental variables to gmap and gsnap
 
|-
 
|-
 
|gmes
 
|gmes
 
|v2.3e
 
|v2.3e
 +
|
 +
|adds environmental variables to gmes
 
|-
 
|-
 
|gnuplot
 
|gnuplot
 
|4.6.3
 
|4.6.3
 +
|
 +
|Description of the module: Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms
 
|-
 
|-
 
|graphviz
 
|graphviz
 
|2.32.0
 
|2.32.0
 +
|
 +
|www.graphviz.org Graphviz is open source graph visualization software.
 
|-
 
|-
 
|gsl
 
|gsl
 
|1.16
 
|1.16
 +
|http://www.gnu.org/software/gsl/
 +
|The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.  The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
 
|-
 
|-
 
|hmmer-mpi
 
|hmmer-mpi
 
|2.32-MPI-0.92
 
|2.32-MPI-0.92
 +
|
 +
|adds environmental variables to hmmer-mpi
 
|-
 
|-
 
|hmmer
 
|hmmer
 
|2.3.2, 3.0
 
|2.3.2, 3.0
 +
|http://hmmer.janelia.org/
 +
|HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). -
 
|-
 
|-
 
|htseq
 
|htseq
 
|0.5.4
 
|0.5.4
 +
|http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
 +
|HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
 
|-
 
|-
 
|icc
 
|icc
 
|2013.5.192
 
|2013.5.192
 +
|
 +
|Intel Studio XE 2013
 
|-
 
|-
 
|idba-ud
 
|idba-ud
 
|1.1.0
 
|1.1.0
 +
|
 +
|adds environmental variables to idba-ud
 
|-
 
|-
 
|IGV
 
|IGV
 
|2.1.24
 
|2.1.24
 +
|
 +
|adds environmental variables to IGV
 
|-
 
|-
 
|IGVTools
 
|IGVTools
 
|2.1.24
 
|2.1.24
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|IMAGE
 
|IMAGE
 
|2.33
 
|2.33
 +
|
 +
|adds environmental variables to IMAGE
 
|-
 
|-
 
|ImageMagick
 
|ImageMagick
 
|6.7.8-9
 
|6.7.8-9
 +
|http://www.imagemagick.org
 +
|ImageMagick® is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
 
|-
 
|-
 
|infernal
 
|infernal
 
|1.1rc1, 1.1rc2
 
|1.1rc1, 1.1rc2
 +
|
 +
|adds environmental variables to infernal 1.1 rc1
 
|-
 
|-
 
|inparanoid
 
|inparanoid
 
|4.1
 
|4.1
 +
|
 +
|adds environmental variables for inparanoid
 
|-
 
|-
 
|iprscan
 
|iprscan
 
|4.8, 5.44, 5.45
 
|4.8, 5.44, 5.45
 +
|
 +
|https://code.google.com/p/interproscan/wiki/Introduction Scans a range of protein signatures against your sequence
 +
|-
 +
|
 +
|
 +
|
 +
|It can be used as an ab initio program, which means it bases its prediction purely on the
 
|-
 
|-
 
|java
 
|java
 
|1.6.0_41, 1.7.0_06-i386, 1.7.0_07
 
|1.6.0_41, 1.7.0_06-i386, 1.7.0_07
 +
|
 +
|adds environmental variables to java
 
|-
 
|-
 
|jellyfish
 
|jellyfish
 
|1.1.6, 1.1.11
 
|1.1.6, 1.1.11
 +
|
 +
|http://www.cbcb.umd.edu/software/jellyfish/  JELLYFISH - Fast, Parallel k-mer Counting for DNA
 
|-
 
|-
 
|khmer
 
|khmer
 
|2013-05-06
 
|2013-05-06
 +
|
 +
|adds environmental variables khmer
 
|-
 
|-
 
|kmergenie
 
|kmergenie
 
|1.5854
 
|1.5854
 +
|
 +
|Description of the module
 
|-
 
|-
 
|krona
 
|krona
 
|2.2
 
|2.2
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|lamarc
 
|lamarc
 
|2.1.8
 
|2.1.8
 +
|
 +
|adds environmental variables to cufflinks
 
|-
 
|-
 
|last
 
|last
 
|278
 
|278
 +
|
 +
|adds environmental variables to last
 
|-
 
|-
 
|lastz
 
|lastz
 
|1.02.00
 
|1.02.00
 +
|
 +
|adds environmental variables to lastz
 
|-
 
|-
 
|libstree
 
|libstree
 
|0.4.2
 
|0.4.2
 +
|http://www.icir.org/christian/libstree/
 +
|libstree is a generic suffix tree implementation, written in C. It can handle arbitrary data structures as elements of a string. Unlike most demo implementations, it is not limited to simple ASCII character strings.
 
|-
 
|-
 
|LR-TRIRLS
 
|LR-TRIRLS
 
|20060531
 
|20060531
 +
|http://komarix.org/ac/lr/
 +
|LR-TRIRLS stands for Logistic Regression with Truncated Regularized Iteratively Re-weighted Least Squares. This is our contribution to LR computation.
 
|-
 
|-
 
|lua
 
|lua
 
|5.1.4, 5.2.2
 
|5.1.4, 5.2.2
 +
|
 +
|adds environmental variables to lua
 
|-
 
|-
 
|MACS
 
|MACS
 
|1.4.2, 2.0.10
 
|1.4.2, 2.0.10
 +
|http://liulab.dfci.harvard.edu/MACS/
 +
|Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.
 
|-
 
|-
 
|mafft
 
|mafft
 
|6.953
 
|6.953
 +
|
 +
|adds environmental variables to mafft
 
|-
 
|-
 
|matlab-runtime
 
|matlab-runtime
 
|r2012b
 
|r2012b
 +
|
 +
|http://www.mathworks.com/products/compiler/mcr/ The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed
 
|-
 
|-
 
|matlab
 
|matlab
 
|7.11.0.584
 
|7.11.0.584
 +
|
 +
|adds environmental variables to matlab
 
|-
 
|-
 
|mcl
 
|mcl
 
|12-068
 
|12-068
 +
|
 +
|adds environmental variables to orthomcl
 
|-
 
|-
 
|MEGAN
 
|MEGAN
 
|4.70.4, 5.1.0
 
|4.70.4, 5.1.0
 +
|http://ab.inf.uni-tuebingen.de/software/megan/
 +
|In metagenomics, the aim is to understand the composition and operation of complex microbial consortia in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples.
 
|-
 
|-
 
|meme
 
|meme
 
|4.9.0
 
|4.9.0
 +
|
 +
|adds environmental variables to smrtanalysis-1.4.0
 
|-
 
|-
 
|MetaGeneMark
 
|MetaGeneMark
 
|2010
 
|2010
 +
|
 +
|adds environmental variables to MetaGeneMark
 
|-
 
|-
 
|metAMOS
 
|metAMOS
 
|1.2
 
|1.2
 +
|
 +
|A metagenomic assembly pipeline for AMOS http://treangen.github.com/metAMOS/
 
|-
 
|-
 
|MetaVelvet
 
|MetaVelvet
 
|1.2.02, 1.2.02-kmer245
 
|1.2.02, 1.2.02-kmer245
 +
|
 +
|adds environmental variables to MetaVelvet
 
|-
 
|-
 
|mfinder
 
|mfinder
 
|1.2
 
|1.2
 +
|
 +
|adds environmental variables to mfinder
 
|-
 
|-
 
|mira
 
|mira
 
|3.2.1
 
|3.2.1
 +
|
 +
|adds environmental variables to mira
 
|-
 
|-
 
|MOCAT
 
|MOCAT
 
|1.1
 
|1.1
 +
|
 +
|adds environmental variables for MOCAT
 
|-
 
|-
 
|ModalClust
 
|ModalClust
 
|0.2, 0.3
 
|0.2, 0.3
 +
|
 +
|adds environmental variables to ModalClust
 
|-
 
|-
 
|mothur
 
|mothur
 
|1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1
 
|1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1
 +
|http://www.mothur.org/
 +
|This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.
 
|-
 
|-
 
|mpich
 
|mpich
 
|3.0.4
 
|3.0.4
 +
|http://www.mpich.org/
 +
|MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
 
|-
 
|-
 
|mpich2
 
|mpich2
 
|1.4.1p1, 1.5
 
|1.4.1p1, 1.5
 +
|http://www.mpich.org/
 +
|MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
 
|-
 
|-
 
|msort
 
|msort
 
|1.0
 
|1.0
 +
|
 +
|adds environmental variables to msort
 
|-
 
|-
 
|MUMmer
 
|MUMmer
 
|3.23
 
|3.23
 +
|
 +
|adds environmental variables to MUMmer
 
|-
 
|-
 
|muscle
 
|muscle
 
|3.8.31
 
|3.8.31
 +
|
 +
|adds environmental variables to velvet
 
|-
 
|-
 
|novocraft
 
|novocraft
 
|2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
 
|2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
 +
|
 +
|adds environmental variables to novocraft
 
|-
 
|-
 
|oasas-kmer245
 
|oasas-kmer245
 
|0.2.8
 
|0.2.8
 +
|http://www.ebi.ac.uk/~zerbino/oases/
 +
|Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
 
|-
 
|-
 
|oasas
 
|oasas
 
|0.2.8
 
|0.2.8
 +
|http://www.ebi.ac.uk/~zerbino/oases/
 +
|Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
 
|-
 
|-
 
|OLB
 
|OLB
 
|1.9.4
 
|1.9.4
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|openmpi-intel
 
|openmpi-intel
 
|1.6.3
 
|1.6.3
 +
|http://www.open-mpi.org/
 +
|The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
 
|-
 
|-
 
|openmpi
 
|openmpi
 
|1.4.3, 1.6.3
 
|1.4.3, 1.6.3
 +
|http://www.open-mpi.org/
 +
|The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
 
|-
 
|-
 
|orthomcl
 
|orthomcl
 
|2.0.2, 2.0.7
 
|2.0.2, 2.0.7
 +
|
 +
|adds environmental variables to orthomcl
 
|-
 
|-
 
|paml
 
|paml
 
|4.4
 
|4.4
 +
|
 +
|adds environmental variables to paml
 
|-
 
|-
 
|parallel
 
|parallel
 
|20121122
 
|20121122
 +
|
 +
|adds environmental variables to orthomcl
 
|-
 
|-
 
|pathway-tools
 
|pathway-tools
 
|16.5
 
|16.5
 +
|
 +
|adds environmental variables to pathway-tools
 
|-
 
|-
 
|PBJelly
 
|PBJelly
 
|12.9.14
 
|12.9.14
 +
|
 +
|adds environmental variables to PBJelly with smrtanalysis-1.4.0
 
|-
 
|-
 
|peaksplitter
 
|peaksplitter
 
|1.0
 
|1.0
 +
|
 +
|adds environmental variables to peaksplitter
 
|-
 
|-
 
|perfsuite
 
|perfsuite
 
|1.0.0
 
|1.0.0
 +
|
 +
|adds environmental variables to perfsuite
 
|-
 
|-
 
|perl
 
|perl
 
|5.16.1
 
|5.16.1
 +
|http://www.perl.org
 +
|Perl 5 is a highly capable, feature-rich programming language with over 25 years of development. Perl 5 runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
 
|-
 
|-
 
|pfamscan
 
|pfamscan
 
|1.0
 
|1.0
 +
|
 +
|ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/
 
|-
 
|-
 
|phred
 
|phred
 
|0.020425.c
 
|0.020425.c
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|phylip
 
|phylip
 
|3.69
 
|3.69
 +
|
 +
|adds environmental variables to phylip
 
|-
 
|-
 
|phymmbl
 
|phymmbl
 
|4.0
 
|4.0
 +
|
 +
|adds environmental variables to phymmbl
 
|-
 
|-
 
|picard-tools
 
|picard-tools
 
|1.34, 1.73, 1.90
 
|1.34, 1.73, 1.90
 +
|
 +
|adds environmental variables to picard-tools
 
|-
 
|-
 
|polyphen
 
|polyphen
 
|2.2.2
 
|2.2.2
 +
|
 +
|PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
 
|-
 
|-
 
|pplacer
 
|pplacer
 
|1.0, 1.1
 
|1.0, 1.1
 +
|
 +
|adds environmental variables to pplacer
 
|-
 
|-
 
|prank
 
|prank
 
|121002
 
|121002
 +
|
 +
|adds environmental variables to prank
 
|-
 
|-
 
|prodigal
 
|prodigal
 
|2.0, 2.2
 
|2.0, 2.2
 +
|
 +
|adds environmental variables to prodigal
 
|-
 
|-
 
|python
 
|python
−
|2.6.6, 2.7.3(default), 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
+
|2.6.6, 2.7.3, 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
 +
|
 +
|adds environmental variables to Python 3.2
 
|-
 
|-
 
|qiime
 
|qiime
 
|1.3.0, 1.5.0, 1.6.0, 1.7.0
 
|1.3.0, 1.5.0, 1.6.0, 1.7.0
 +
|
 +
|Loads qiimes environmental variables
 
|-
 
|-
 
|quake
 
|quake
 
|0.3.4
 
|0.3.4
 +
|http://www.cbcb.umd.edu/software/quake/
 +
|Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
 
|-
 
|-
 
|quast
 
|quast
 
|2.2
 
|2.2
 +
|
 +
|http://bioinf.spbau.ru/quast QUAST: Quality Assessment Tool for Genome Assemblies
 
|-
 
|-
 
|quest
 
|quest
 
|alpha, devel
 
|alpha, devel
 +
|
 +
|adds environmental variables for EFI QUEST development branch
 
|-
 
|-
 
|R
 
|R
−
|2.15.0, 2.15.1, 2.15.2, 3.0.0(default), 3.0.2
+
|2.15.0, 2.15.1, 2.15.2, 3.0.0, 3.0.2
 +
|http://www.r-project.org/
 +
|R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.
 
|-
 
|-
 
|RAxML
 
|RAxML
 
|7.3.0
 
|7.3.0
 +
|http://sco.h-its.org/exelixis/software.html
 +
|RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
 
|-
 
|-
 
|ray
 
|ray
 
|2.20, 2.30
 
|2.20, 2.30
 +
|
 +
|Ray -- Parallel genome assemblies for parallel DNA sequencing denovoassembler.sourceforge.net/index.html
 
|-
 
|-
 
|rdp_classifier
 
|rdp_classifier
 
|2.5
 
|2.5
 +
|http://rdp.cme.msu.edu/
 +
|The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
 
|-
 
|-
 
|rdxplorer
 
|rdxplorer
 
|3.2
 
|3.2
 +
|
 +
|adds environmental variables rdexplorer. use 'python rdxplorer.py to run'
 
|-
 
|-
 
|repeatmasker
 
|repeatmasker
 
|3.28
 
|3.28
 +
|
 +
|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences
 
|-
 
|-
 
|rockhopper
 
|rockhopper
 
|1.2
 
|1.2
 +
|
 +
|Description of the module Rockhopper, Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data ttp://cs.wellesley.edu/~btjaden/Rockhopper/
 
|-
 
|-
 
|rsa-tools
 
|rsa-tools
 
|2012-10-09
 
|2012-10-09
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|rstudio
 
|rstudio
 
|0.97.312
 
|0.97.312
 +
|
 +
|adds environmental variables to R
 
|-
 
|-
 
|ruby
 
|ruby
 
|1.9.3
 
|1.9.3
 +
|
 +
|adds environmental variables to ruby
 
|-
 
|-
 
|samtools
 
|samtools
 
|0.1.16, 0.1.18, 0.1.19
 
|0.1.16, 0.1.18, 0.1.19
 +
|
 +
|http://sourceforge.net/projects/samtools/files/
 
|-
 
|-
 
|sam_comp
 
|sam_comp
 
|0.7
 
|0.7
 +
|
 +
|adds environmental variables Python 2.7.3
 +
|-
 +
|
 +
|
 +
|
 +
|sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
 
|-
 
|-
 
|SICER
 
|SICER
 
|1.1
 
|1.1
 +
|
 +
|A clustering approach for identification of enriched domains from histone modification ChIP-Seq data http://home.gwu.edu/~wpeng/Software.htm
 
|-
 
|-
 
|signalp
 
|signalp
 
|4.1
 
|4.1
 +
|
 +
|adds environmental variables to perl
 
|-
 
|-
 
|smrtanalysis
 
|smrtanalysis
 
|1.4.0, 2.0.1
 
|1.4.0, 2.0.1
 +
|http://pacbiodevnet.com/
 +
|SMRT Analysis is a bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences. This repository contains a link to download and view the SMRT Analysis source code. It is provided here for reference only and is currently not buildable.
 
|-
 
|-
 
|SnpEff
 
|SnpEff
 
|3.2, 3.3e
 
|3.2, 3.3e
 +
|
 +
|Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). Homepage - http://snpeff.sourceforge.net/
 
|-
 
|-
 
|SOAP2
 
|SOAP2
 
|2.2
 
|2.2
 +
|
 +
|adds environmental variables to SOAP2
 
|-
 
|-
 
|SOAPdenovo-Trans
 
|SOAPdenovo-Trans
 
|1.02
 
|1.02
 +
|http://soap.genomics.org.cn/SOAPdenovo-Trans.html
 +
|SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.
 
|-
 
|-
 
|SOAPdenovo
 
|SOAPdenovo
 
|2.04
 
|2.04
 +
|
 +
|adds environmental variables to SOAPdenovo
 
|-
 
|-
 
|SOAPdenovo2
 
|SOAPdenovo2
 
|r240
 
|r240
 +
|
 +
|adds environmental variables to SOAPdenovo2
 
|-
 
|-
 
|SOAPec
 
|SOAPec
 
|2.01, 2.02
 
|2.01, 2.02
 +
|
 +
|http://soap.genomics.org.cn/about.html
 
|-
 
|-
 
|SOAPErrorCorrection
 
|SOAPErrorCorrection
 
|0.04
 
|0.04
 +
|
 +
|adds environmental variables to SOAPErrorCorrection
 
|-
 
|-
 
|SOAPGapCloser
 
|SOAPGapCloser
 
|1.12
 
|1.12
 +
|
 +
|adds environmental variables to SOAPGapCloser
 
|-
 
|-
 
|SOAPprepare
 
|SOAPprepare
 
|0.1
 
|0.1
 +
|
 +
|adds environmental variables to SOAPdenovo
 
|-
 
|-
 
|speciateit
 
|speciateit
−
|184(default)
+
|184
 +
|http://sourceforge.net/p/speciateit/code/HEAD/tree/
 +
|This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
 
|-
 
|-
 
|speciate_it
 
|speciate_it
−
|184(default)
+
|184
 +
|http://sourceforge.net/p/speciateit/code/HEAD/tree/
 +
|This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
 
|-
 
|-
 
|sratoolkit
 
|sratoolkit
 
|2.1.16
 
|2.1.16
 +
|
 +
|adds environmental variables to sratoolkit
 
|-
 
|-
 
|srna-tools
 
|srna-tools
 
|20130118
 
|20130118
 +
|
 +
|adds environmental variables to srna-tools
 
|-
 
|-
 
|ssaha2
 
|ssaha2
 
|2.5.5
 
|2.5.5
 +
|
 +
|http://www.sanger.ac.uk/resources/software/ssaha2/SSAHA2:%20Sequence%20Search%20and%20Alignment%20by%20Hashing%20Algorithm
 
|-
 
|-
 
|stacks
 
|stacks
 
|0.9996, 0.99994
 
|0.9996, 0.99994
 +
|
 +
|adds environmental variables to stacks
 
|-
 
|-
 
|structure
 
|structure
 
|2.3.4
 
|2.3.4
 +
|http://pritch.bsd.uchicago.edu/structure.html
 +
|The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
 
|-
 
|-
 
|subread
 
|subread
 
|3.1.6
 
|3.1.6
 +
|
 +
|Fast, accurate and scalable read mapping by seed-and-vote http://sourceforge.net/projects/subread/
 +
|-
 +
|
 +
|
 +
|
 +
|such as EST, MS/MS, protein alignments and synthenic genomic alignments.
 
|-
 
|-
 
|supfam
 
|supfam
 
|1.75
 
|1.75
 +
|
 +
|produce SCOP protein domain assignments using the SUPERFAMILY hidden Markov models (HMMs) and associated scripts.
 
|-
 
|-
 
|tabix
 
|tabix
 
|0.2.6
 
|0.2.6
 +
|http://samtools.sourceforge.net/tabix.shtml
 +
|Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
 
|-
 
|-
 
|tcoffee
 
|tcoffee
 
|10-r1613
 
|10-r1613
 +
|
 +
|Description of the module http://www.tcoffee.org/
 
|-
 
|-
 
|tmhmm
 
|tmhmm
 
|2.0
 
|2.0
 +
|
 +
|adds environmental variables to tmhmm
 
|-
 
|-
 
|tophat
 
|tophat
 
|1.4.1
 
|1.4.1
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|tophat2
 
|tophat2
−
|2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10(default)
+
|2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10
 +
|
 +
|adds environmental variables to tophat 2
 
|-
 
|-
 
|treemix
 
|treemix
 
|1.12
 
|1.12
 +
|http://code.google.com/p/treemix/
 +
|TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
 
|-
 
|-
 
|trf
 
|trf
 
|4.04
 
|4.04
 +
|
 +
|adds environmental variables to trf
 
|-
 
|-
 
|trimmomatic
 
|trimmomatic
 
|0.22, 0.27, 0.30
 
|0.22, 0.27, 0.30
 +
|
 +
|adds environmental variables to trimmomatic
 
|-
 
|-
 
|trinityrnaseq-intel
 
|trinityrnaseq-intel
 
|r2013-02-25
 
|r2013-02-25
 +
|http://trinityrnaseq.sourceforge.net/
 +
|Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
 
|-
 
|-
 
|trinityrnaseq
 
|trinityrnaseq
 
|r2012-06-08, r2013-02-25, r2013-08-14
 
|r2012-06-08, r2013-02-25, r2013-08-14
 +
|http://trinityrnaseq.sourceforge.net/
 +
|Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
 
|-
 
|-
 
|trinotate
 
|trinotate
 
|trinotate_r20130826
 
|trinotate_r20130826
 +
|
 +
|Description of the module
 
|-
 
|-
 
|truesight
 
|truesight
 
|0.06
 
|0.06
 +
|http://bioen-compbio.bioen.illinois.edu/TrueSight/
 +
|TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq.
 
|-
 
|-
 
|uchime
 
|uchime
 
|4.2.40
 
|4.2.40
 +
|
 +
|adds environmental variables to uchime
 
|-
 
|-
 
|usearch
 
|usearch
 
|6.0.307, 6.1.544, 7.0.959
 
|6.0.307, 6.1.544, 7.0.959
 +
|http://www.drive5.com/usearch/
 +
|USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
 
|-
 
|-
 
|USeq
 
|USeq
 
|8.5.1
 
|8.5.1
 +
|
 +
|adds environmental variables to USeq
 
|-
 
|-
 
|vcftools
 
|vcftools
 
|0.1.7, 0.1.11
 
|0.1.7, 0.1.11
 +
|http://vcftools.sourceforge.net/index.html
 +
|Welcome to VCFtools - 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-kmer245
 
|velvet-kmer245
 
|1.2.10
 
|1.2.10
 +
|http://www.ebi.ac.uk/~zerbino/velvet/
 +
|Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
 
|-
 
|-
 
|velvet
 
|velvet
 
|1.1.04, 1.2.08, 1.2.10
 
|1.1.04, 1.2.08, 1.2.10
 +
|http://www.ebi.ac.uk/~zerbino/velvet/
 +
|Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
 
|-
 
|-
 
|velvetOptimiser
 
|velvetOptimiser
 
|2.2.5
 
|2.2.5
 +
|
 +
|http://bioinformatics.net.au/software.velvetoptimiser.shtml  VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
 
|-
 
|-
 
|wessim
 
|wessim
 
|1.0
 
|1.0
 +
|
 +
|RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of lar$
 
|-
 
|-
 
|wgs
 
|wgs
 
|7.0
 
|7.0
 +
|
 +
|adds environmental variables to qiime and qiime
 
|-
 
|-
 
|wise
 
|wise
 
|2.2.3-rc7
 
|2.2.3-rc7
 +
|
 +
|adds environmental variables to wise
 
|}
 
|}

Revision as of 09:40, 17 February 2014

Application Installed Versions
, , , , , , , , , , , , , , , , , , , , ,
454 2.6, 2.7, 2.8 adds environmental variables to 454
AbundantOTU+ 0.91b adds environmental variables to AbundantOTU+
abyss 1.2.5, 1.3.3, 1.3.4 adds environmental variables to ABySS
afni 2011_12_21_2014 adds environmental variables to afni
allpathslg 42911 adds environmental variables for allpathslg
amos 3.1.0 http://sourceforge.net/apps/mediawiki/amos The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler.
AmpliconNoise 1.2.7 adds environmental variables to AmpliconNoise
art 20110922 adds environmental variables to afni
artemis 14.0 adds environmental variables to artemis
augustus 2.6.1
AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller.
b2g4pipe 2.5 adds environmental variables to blast2go pipe
babraham bioinformatics Description of the module
bali-phy 2.1.1 adds environmental variables to bali-phy
bam2fastq 1.1.0 adds environmental variables to qiime and qiime
bamtools 0.9.0 adds environmental variables to qiime and qiime
bcbio-nextgen 0.6.5 A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. Homepage - https://bcbio-nextgen.readthedocs.org
bedtools 2.10.0, 2.10.1, 2.17.0 adds environmental variables to bedtools
biodatabase 1.0 adds environmental variables to biodatabase scripts
biopieces 0.48 adds environmental variables, software, and bins to biopieces
blast+ 2.2.25+, 2.2.28+ adds environmental variables to qiime and qiime
blast-intel 2.2.26 http://blast.ncbi.nlm.nih.gov/Blast.cgi The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
blast 2.2.25, 2.2.26 adds environmental variables to qiime and qiime
blast2go 2.5 Description of the module
blat 0.34 adds environmental variables to blat
boost-intel 1.54 http://www.boost.org/ Boost provides free peer-reviewed portable C++ source libraries.
boost 1.54 http://www.boost.org/ Boost provides free peer-reviewed portable C++ source libraries.
bowtie 0.12.8, 0.12.9, 1.0.0 http://bowtie-bio.sourceforge.net Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
bowtie2 2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0 adds environmental variables to Bowtie2
breseq 0.24 {Determine mutations in evolved microbes from next-generation sequencing data. http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing
bwa 0.5.9, 0.7.5a bio-bwa.sourceforge.net BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome
cafe 2.2, 3.0 adds environmental variables to cafe
casava 1.8.2 adds environmental variables to casava
cd-hit 4.6, 4.6.1 CD-HIT Suite http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide
cdbfasta 0.99 http://cdbfasta.sourceforge.net/ fast indexing and retrieval of fasta records from flat file databases.
chance 1.0 CHANCE - CHip-seq ANalytics and Confidence Estimation. songlab.ucsf.edu/Software.html
chimera 1.5.3, 1.6.2 adds environmental variables for chimera
cisgenome 2.0 http://www.biostat.jhsph.edu/~hji/cisgenome/ An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
ClonalFrame 1.2 adds environmental variables to ClonalFrame
clustalo 1.2.0 Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. clustal.org/omega
clustalw 2.1 adds environmental variables to clustalw
cufflinks 1.1.0, 1.3.0, 2.0.2, 2.1.1 adds environmental variables to cufflinks
cutadapt 1.2 https://code.google.com/p/cutadapt/ cutadapt removes adapter sequences from high-throughput sequencing data.
cytoscape 2.8.1, 2.8.3 adds environmental variables to cytoscape
EagleView 2.2 adds environmental variables to EagleView
efiest alpha, devel adds environmental variables for EFI QUEST development branch
EMBOSS 6.5.7 adds environmental variables to EMBOSS
erange 3.2.1 adds environmental variables to qiime and qiime
estscan 3.0.3 adds environmental variables to qiime and qiime
fasta 36.3.5d adds environmental variables to qiime and qiime
fasta_splitter 1 Description of the module
fastqc 0.10.1 adds environmental variables to fastqc
fastsimcoal2 1.1.1 http://cmpg.unibe.ch/software/fastsimcoal2/ fast sequential Markov coalescent simulation of genomic data under complex evolutionary models.
fasttree 2.1.7 http://www.microbesonline.org/fasttree/ Infers ML phylogenetic trees from alignments
fastx_toolkit 0.0.13 adds environmental variables to fastx_toolkit
findpeaks 3.1.9.2 adds environmental variables to findpeaks
freebayes 0.9.6 adds environmental variables to freebayes
gatk 1.6-5, 1.6-13, 2.5-2, 2.6-4 http://www.broadinstitute.org/gatk The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gcc 4.8.1 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system. The GNU system was developed to be 100% free software, free in the sense that it respects the user's freedom. Homepage : http://gcc.gnu.org
geneid 1.0 adds environmental variables to geneid
genomer 0.0.10 adds environmental variables to usearch
genometools 1.5.1 http://genometools.org/ The GenomeTools genome analysis system is a free 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.
gff 2.1 Description of the module
glimmer 3.02 adds environmental variables to bedtools
gmap 2011-09-14, 2013-03-31 adds environmental variables to gmap and gsnap
gmes v2.3e adds environmental variables to gmes
gnuplot 4.6.3 Description of the module: Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms
graphviz 2.32.0 www.graphviz.org Graphviz is open source graph visualization software.
gsl 1.16 http://www.gnu.org/software/gsl/ The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
hmmer-mpi 2.32-MPI-0.92 adds environmental variables to hmmer-mpi
hmmer 2.3.2, 3.0 http://hmmer.janelia.org/ HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). -
htseq 0.5.4 http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
icc 2013.5.192 Intel Studio XE 2013
idba-ud 1.1.0 adds environmental variables to idba-ud
IGV 2.1.24 adds environmental variables to IGV
IGVTools 2.1.24 adds environmental variables to qiime and qiime
IMAGE 2.33 adds environmental variables to IMAGE
ImageMagick 6.7.8-9 http://www.imagemagick.org ImageMagick® is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
infernal 1.1rc1, 1.1rc2 adds environmental variables to infernal 1.1 rc1
inparanoid 4.1 adds environmental variables for inparanoid
iprscan 4.8, 5.44, 5.45 https://code.google.com/p/interproscan/wiki/Introduction Scans a range of protein signatures against your sequence
It can be used as an ab initio program, which means it bases its prediction purely on the
java 1.6.0_41, 1.7.0_06-i386, 1.7.0_07 adds environmental variables to java
jellyfish 1.1.6, 1.1.11 http://www.cbcb.umd.edu/software/jellyfish/ JELLYFISH - Fast, Parallel k-mer Counting for DNA
khmer 2013-05-06 adds environmental variables khmer
kmergenie 1.5854 Description of the module
krona 2.2 adds environmental variables to qiime and qiime
lamarc 2.1.8 adds environmental variables to cufflinks
last 278 adds environmental variables to last
lastz 1.02.00 adds environmental variables to lastz
libstree 0.4.2 http://www.icir.org/christian/libstree/ libstree is a generic suffix tree implementation, written in C. It can handle arbitrary data structures as elements of a string. Unlike most demo implementations, it is not limited to simple ASCII character strings.
LR-TRIRLS 20060531 http://komarix.org/ac/lr/ LR-TRIRLS stands for Logistic Regression with Truncated Regularized Iteratively Re-weighted Least Squares. This is our contribution to LR computation.
lua 5.1.4, 5.2.2 adds environmental variables to lua
MACS 1.4.2, 2.0.10 http://liulab.dfci.harvard.edu/MACS/ Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.
mafft 6.953 adds environmental variables to mafft
matlab-runtime r2012b http://www.mathworks.com/products/compiler/mcr/ The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed
matlab 7.11.0.584 adds environmental variables to matlab
mcl 12-068 adds environmental variables to orthomcl
MEGAN 4.70.4, 5.1.0 http://ab.inf.uni-tuebingen.de/software/megan/ In metagenomics, the aim is to understand the composition and operation of complex microbial consortia in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples.
meme 4.9.0 adds environmental variables to smrtanalysis-1.4.0
MetaGeneMark 2010 adds environmental variables to MetaGeneMark
metAMOS 1.2 A metagenomic assembly pipeline for AMOS http://treangen.github.com/metAMOS/
MetaVelvet 1.2.02, 1.2.02-kmer245 adds environmental variables to MetaVelvet
mfinder 1.2 adds environmental variables to mfinder
mira 3.2.1 adds environmental variables to mira
MOCAT 1.1 adds environmental variables for MOCAT
ModalClust 0.2, 0.3 adds environmental variables to ModalClust
mothur 1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1 http://www.mothur.org/ This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.
mpich 3.0.4 http://www.mpich.org/ MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
mpich2 1.4.1p1, 1.5 http://www.mpich.org/ MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
msort 1.0 adds environmental variables to msort
MUMmer 3.23 adds environmental variables to MUMmer
muscle 3.8.31 adds environmental variables to velvet
novocraft 2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02 adds environmental variables to novocraft
oasas-kmer245 0.2.8 http://www.ebi.ac.uk/~zerbino/oases/ Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
oasas 0.2.8 http://www.ebi.ac.uk/~zerbino/oases/ Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
OLB 1.9.4 adds environmental variables to qiime and qiime
openmpi-intel 1.6.3 http://www.open-mpi.org/ The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
openmpi 1.4.3, 1.6.3 http://www.open-mpi.org/ The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
orthomcl 2.0.2, 2.0.7 adds environmental variables to orthomcl
paml 4.4 adds environmental variables to paml
parallel 20121122 adds environmental variables to orthomcl
pathway-tools 16.5 adds environmental variables to pathway-tools
PBJelly 12.9.14 adds environmental variables to PBJelly with smrtanalysis-1.4.0
peaksplitter 1.0 adds environmental variables to peaksplitter
perfsuite 1.0.0 adds environmental variables to perfsuite
perl 5.16.1 http://www.perl.org Perl 5 is a highly capable, feature-rich programming language with over 25 years of development. Perl 5 runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
pfamscan 1.0 ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/
phred 0.020425.c adds environmental variables to qiime and qiime
phylip 3.69 adds environmental variables to phylip
phymmbl 4.0 adds environmental variables to phymmbl
picard-tools 1.34, 1.73, 1.90 adds environmental variables to picard-tools
polyphen 2.2.2 PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
pplacer 1.0, 1.1 adds environmental variables to pplacer
prank 121002 adds environmental variables to prank
prodigal 2.0, 2.2 adds environmental variables to prodigal
python 2.6.6, 2.7.3, 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3 adds environmental variables to Python 3.2
qiime 1.3.0, 1.5.0, 1.6.0, 1.7.0 Loads qiimes environmental variables
quake 0.3.4 http://www.cbcb.umd.edu/software/quake/ Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
quast 2.2 http://bioinf.spbau.ru/quast QUAST: Quality Assessment Tool for Genome Assemblies
quest alpha, devel adds environmental variables for EFI QUEST development branch
R 2.15.0, 2.15.1, 2.15.2, 3.0.0, 3.0.2 http://www.r-project.org/ R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.
RAxML 7.3.0 http://sco.h-its.org/exelixis/software.html RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
ray 2.20, 2.30 Ray -- Parallel genome assemblies for parallel DNA sequencing denovoassembler.sourceforge.net/index.html
rdp_classifier 2.5 http://rdp.cme.msu.edu/ The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
rdxplorer 3.2 adds environmental variables rdexplorer. use 'python rdxplorer.py to run'
repeatmasker 3.28 RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences
rockhopper 1.2 Description of the module Rockhopper, Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data ttp://cs.wellesley.edu/~btjaden/Rockhopper/
rsa-tools 2012-10-09 adds environmental variables to qiime and qiime
rstudio 0.97.312 adds environmental variables to R
ruby 1.9.3 adds environmental variables to ruby
samtools 0.1.16, 0.1.18, 0.1.19 http://sourceforge.net/projects/samtools/files/
sam_comp 0.7 adds environmental variables Python 2.7.3
sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources
SICER 1.1 A clustering approach for identification of enriched domains from histone modification ChIP-Seq data http://home.gwu.edu/~wpeng/Software.htm
signalp 4.1 adds environmental variables to perl
smrtanalysis 1.4.0, 2.0.1 http://pacbiodevnet.com/ SMRT Analysis is a bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences. This repository contains a link to download and view the SMRT Analysis source code. It is provided here for reference only and is currently not buildable.
SnpEff 3.2, 3.3e Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). Homepage - http://snpeff.sourceforge.net/
SOAP2 2.2 adds environmental variables to SOAP2
SOAPdenovo-Trans 1.02 http://soap.genomics.org.cn/SOAPdenovo-Trans.html SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.
SOAPdenovo 2.04 adds environmental variables to SOAPdenovo
SOAPdenovo2 r240 adds environmental variables to SOAPdenovo2
SOAPec 2.01, 2.02 http://soap.genomics.org.cn/about.html
SOAPErrorCorrection 0.04 adds environmental variables to SOAPErrorCorrection
SOAPGapCloser 1.12 adds environmental variables to SOAPGapCloser
SOAPprepare 0.1 adds environmental variables to SOAPdenovo
speciateit 184 http://sourceforge.net/p/speciateit/code/HEAD/tree/ This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
speciate_it 184 http://sourceforge.net/p/speciateit/code/HEAD/tree/ This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
sratoolkit 2.1.16 adds environmental variables to sratoolkit
srna-tools 20130118 adds environmental variables to srna-tools
ssaha2 2.5.5 http://www.sanger.ac.uk/resources/software/ssaha2/SSAHA2:%20Sequence%20Search%20and%20Alignment%20by%20Hashing%20Algorithm
stacks 0.9996, 0.99994 adds environmental variables to stacks
structure 2.3.4 http://pritch.bsd.uchicago.edu/structure.html The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
subread 3.1.6 Fast, accurate and scalable read mapping by seed-and-vote http://sourceforge.net/projects/subread/
such as EST, MS/MS, protein alignments and synthenic genomic alignments.
supfam 1.75 produce SCOP protein domain assignments using the SUPERFAMILY hidden Markov models (HMMs) and associated scripts.
tabix 0.2.6 http://samtools.sourceforge.net/tabix.shtml Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
tcoffee 10-r1613 Description of the module http://www.tcoffee.org/
tmhmm 2.0 adds environmental variables to tmhmm
tophat 1.4.1 adds environmental variables to qiime and qiime
tophat2 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10 adds environmental variables to tophat 2
treemix 1.12 http://code.google.com/p/treemix/ TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
trf 4.04 adds environmental variables to trf
trimmomatic 0.22, 0.27, 0.30 adds environmental variables to trimmomatic
trinityrnaseq-intel r2013-02-25 http://trinityrnaseq.sourceforge.net/ Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
trinityrnaseq r2012-06-08, r2013-02-25, r2013-08-14 http://trinityrnaseq.sourceforge.net/ Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
trinotate trinotate_r20130826 Description of the module
truesight 0.06 http://bioen-compbio.bioen.illinois.edu/TrueSight/ TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq.
uchime 4.2.40 adds environmental variables to uchime
usearch 6.0.307, 6.1.544, 7.0.959 http://www.drive5.com/usearch/ USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
USeq 8.5.1 adds environmental variables to USeq
vcftools 0.1.7, 0.1.11 http://vcftools.sourceforge.net/index.html Welcome to VCFtools - 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-kmer245 1.2.10 http://www.ebi.ac.uk/~zerbino/velvet/ Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
velvet 1.1.04, 1.2.08, 1.2.10 http://www.ebi.ac.uk/~zerbino/velvet/ Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
velvetOptimiser 2.2.5 http://bioinformatics.net.au/software.velvetoptimiser.shtml VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
wessim 1.0 RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of lar$
wgs 7.0 adds environmental variables to qiime and qiime
wise 2.2.3-rc7 adds environmental variables to wise
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