Difference between revisions of "Biocluster Applications"
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!Application | !Application | ||
!Installed Versions | !Installed Versions | ||
| − | |||
!Description | !Description | ||
|- | |- | ||
|454 | |454 | ||
|2.6, 2.7, 2.8 | |2.6, 2.7, 2.8 | ||
| − | |||
|adds environmental variables to 454 | |adds environmental variables to 454 | ||
|- | |- | ||
|AbundantOTU+ | |AbundantOTU+ | ||
|0.91b | |0.91b | ||
| − | |||
|adds environmental variables to AbundantOTU+ | |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 | |adds environmental variables to ABySS | ||
|- | |- | ||
|afni | |afni | ||
|2011_12_21_2014 | |2011_12_21_2014 | ||
| − | |||
|adds environmental variables to afni | |adds environmental variables to afni | ||
|- | |- | ||
|allpathslg | |allpathslg | ||
|42911 | |42911 | ||
| − | |||
|adds environmental variables for allpathslg | |adds environmental variables for allpathslg | ||
|- | |- | ||
| − | |amos | + | |[amos http://sourceforge.net/apps/mediawiki/amos] |
|3.1.0 | |3.1.0 | ||
| − | |||
|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. | |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 | |adds environmental variables to AmpliconNoise | ||
|- | |- | ||
|art | |art | ||
|20110922 | |20110922 | ||
| − | |||
|adds environmental variables to afni | |adds environmental variables to afni | ||
|- | |- | ||
|artemis | |artemis | ||
|14.0 | |14.0 | ||
| − | |||
|adds environmental variables to artemis | |adds environmental variables to artemis | ||
|- | |- | ||
|augustus | |augustus | ||
|2.6.1 | |2.6.1 | ||
| − | |||
| | | | ||
|- | |- | ||
|b2g4pipe | |b2g4pipe | ||
|2.5 | |2.5 | ||
| − | |||
|adds environmental variables to blast2go pipe | |adds environmental variables to blast2go pipe | ||
|- | |- | ||
|babraham | |babraham | ||
|bioinformatics | |bioinformatics | ||
| − | |||
|Description of the module | |Description of the module | ||
|- | |- | ||
|bali-phy | |bali-phy | ||
|2.1.1 | |2.1.1 | ||
| − | |||
|adds environmental variables to bali-phy | |adds environmental variables to bali-phy | ||
|- | |- | ||
|bam2fastq | |bam2fastq | ||
|1.1.0 | |1.1.0 | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|bamtools | |bamtools | ||
|0.9.0 | |0.9.0 | ||
| − | |||
|adds environmental variables to qiime and qiime | |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 | |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 | |adds environmental variables to bedtools | ||
|- | |- | ||
|biodatabase | |biodatabase | ||
|1.0 | |1.0 | ||
| − | |||
|adds environmental variables to biodatabase scripts | |adds environmental variables to biodatabase scripts | ||
|- | |- | ||
|biopieces | |biopieces | ||
|0.48 | |0.48 | ||
| − | |||
|adds environmental variables, software, and bins to biopieces | |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 | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
| − | |blast-intel | + | |[blast-intel http://blast.ncbi.nlm.nih.gov/Blast.cgi] |
|2.2.26 | |2.2.26 | ||
| − | |||
|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. | |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 | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|blast2go | |blast2go | ||
|2.5 | |2.5 | ||
| − | |||
|Description of the module | |Description of the module | ||
|- | |- | ||
|blat | |blat | ||
|0.34 | |0.34 | ||
| − | |||
|adds environmental variables to blat | |adds environmental variables to blat | ||
|- | |- | ||
| − | |boost-intel | + | |[boost-intel http://www.boost.org/] |
|1.54 | |1.54 | ||
| − | |||
|Boost provides free peer-reviewed portable C++ source libraries. | |Boost provides free peer-reviewed portable C++ source libraries. | ||
|- | |- | ||
| − | |boost | + | |[boost http://www.boost.org/] |
|1.54 | |1.54 | ||
| − | |||
|Boost provides free peer-reviewed portable C++ source libraries. | |Boost provides free peer-reviewed portable C++ source libraries. | ||
|- | |- | ||
| − | |bowtie | + | |[bowtie http://bowtie-bio.sourceforge.net] |
|0.12.8, 0.12.9, 1.0.0 | |0.12.8, 0.12.9, 1.0.0 | ||
| − | |||
|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). | |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 | |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 | |{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 | |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 | |adds environmental variables to cafe | ||
|- | |- | ||
|casava | |casava | ||
|1.8.2 | |1.8.2 | ||
| − | |||
|adds environmental variables to casava | |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 | |CD-HIT Suite http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit_user_guide | ||
|- | |- | ||
| − | |cdbfasta | + | |[cdbfasta http://cdbfasta.sourceforge.net/] |
|0.99 | |0.99 | ||
| − | |||
|fast indexing and retrieval of fasta records from flat file databases. | |fast indexing and retrieval of fasta records from flat file databases. | ||
|- | |- | ||
|chance | |chance | ||
|1.0 | |1.0 | ||
| − | |||
|CHANCE - CHip-seq ANalytics and Confidence Estimation. songlab.ucsf.edu/Software.html | |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 | |adds environmental variables for chimera | ||
|- | |- | ||
| − | |cisgenome | + | |[cisgenome http://www.biostat.jhsph.edu/~hji/cisgenome/] |
|2.0 | |2.0 | ||
| − | |||
|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | |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 | |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 | |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 | |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 | |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. | |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 | |adds environmental variables to cytoscape | ||
|- | |- | ||
|EagleView | |EagleView | ||
|2.2 | |2.2 | ||
| − | |||
|adds environmental variables to EagleView | |adds environmental variables to EagleView | ||
|- | |- | ||
|efiest | |efiest | ||
|alpha, devel | |alpha, devel | ||
| − | |||
|adds environmental variables for EFI QUEST development branch | |adds environmental variables for EFI QUEST development branch | ||
|- | |- | ||
|EMBOSS | |EMBOSS | ||
|6.5.7 | |6.5.7 | ||
| − | |||
|adds environmental variables to EMBOSS | |adds environmental variables to EMBOSS | ||
|- | |- | ||
|erange | |erange | ||
|3.2.1 | |3.2.1 | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|estscan | |estscan | ||
|3.0.3 | |3.0.3 | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|fasta | |fasta | ||
|36.3.5d | |36.3.5d | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|fasta_splitter | |fasta_splitter | ||
|1 | |1 | ||
| − | |||
|Description of the module | |Description of the module | ||
|- | |- | ||
|fastqc | |fastqc | ||
|0.10.1 | |0.10.1 | ||
| − | |||
|adds environmental variables to fastqc | |adds environmental variables to fastqc | ||
|- | |- | ||
| − | |fastsimcoal2 | + | |[fastsimcoal2 http://cmpg.unibe.ch/software/fastsimcoal2/] |
|1.1.1 | |1.1.1 | ||
| − | |||
|fast sequential Markov coalescent simulation of genomic data under complex evolutionary models. | |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 | |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 | |adds environmental variables to fastx_toolkit | ||
|- | |- | ||
|findpeaks | |findpeaks | ||
|3.1.9.2 | |3.1.9.2 | ||
| − | |||
|adds environmental variables to findpeaks | |adds environmental variables to findpeaks | ||
|- | |- | ||
|freebayes | |freebayes | ||
|0.9.6 | |0.9.6 | ||
| − | |||
|adds environmental variables to freebayes | |adds environmental variables to freebayes | ||
|- | |- | ||
| − | |gatk | + | |[gatk http://www.broadinstitute.org/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 | ||
| − | |||
|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. | |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 | |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 | |adds environmental variables to geneid | ||
|- | |- | ||
|genomer | |genomer | ||
|0.0.10 | |0.0.10 | ||
| − | |||
|adds environmental variables to usearch | |adds environmental variables to usearch | ||
|- | |- | ||
| − | |genometools | + | |[genometools http://genometools.org/] |
|1.5.1 | |1.5.1 | ||
| − | |||
|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. | |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 | |Description of the module | ||
|- | |- | ||
|glimmer | |glimmer | ||
|3.02 | |3.02 | ||
| − | |||
|adds environmental variables to bedtools | |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 | |adds environmental variables to gmap and gsnap | ||
|- | |- | ||
|gmes | |gmes | ||
|v2.3e | |v2.3e | ||
| − | |||
|adds environmental variables to gmes | |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 | |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. | |www.graphviz.org Graphviz is open source graph visualization software. | ||
|- | |- | ||
| − | |gsl | + | |[gsl http://www.gnu.org/software/gsl/] |
|1.16 | |1.16 | ||
| − | |||
|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. | |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 | |adds environmental variables to hmmer-mpi | ||
|- | |- | ||
| − | |hmmer | + | |[hmmer http://hmmer.janelia.org/] |
|2.3.2, 3.0 | |2.3.2, 3.0 | ||
| − | |||
|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). - | |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 http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] |
|0.5.4 | |0.5.4 | ||
| − | |||
|HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. | |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 | |Intel Studio XE 2013 | ||
|- | |- | ||
|idba-ud | |idba-ud | ||
|1.1.0 | |1.1.0 | ||
| − | |||
|adds environmental variables to idba-ud | |adds environmental variables to idba-ud | ||
|- | |- | ||
|IGV | |IGV | ||
|2.1.24 | |2.1.24 | ||
| − | |||
|adds environmental variables to IGV | |adds environmental variables to IGV | ||
|- | |- | ||
|IGVTools | |IGVTools | ||
|2.1.24 | |2.1.24 | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|IMAGE | |IMAGE | ||
|2.33 | |2.33 | ||
| − | |||
|adds environmental variables to IMAGE | |adds environmental variables to IMAGE | ||
|- | |- | ||
| − | |ImageMagick | + | |[ImageMagick http://www.imagemagick.org] |
|6.7.8-9 | |6.7.8-9 | ||
| − | |||
|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. | |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 | |adds environmental variables to infernal 1.1 rc1 | ||
|- | |- | ||
|inparanoid | |inparanoid | ||
|4.1 | |4.1 | ||
| − | |||
|adds environmental variables for inparanoid | |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 | |https://code.google.com/p/interproscan/wiki/Introduction Scans a range of protein signatures against your sequence | ||
|- | |- | ||
|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 | |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 | |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 | |adds environmental variables khmer | ||
|- | |- | ||
|kmergenie | |kmergenie | ||
|1.5854 | |1.5854 | ||
| − | |||
|Description of the module | |Description of the module | ||
|- | |- | ||
|krona | |krona | ||
|2.2 | |2.2 | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|lamarc | |lamarc | ||
|2.1.8 | |2.1.8 | ||
| − | |||
|adds environmental variables to cufflinks | |adds environmental variables to cufflinks | ||
|- | |- | ||
|last | |last | ||
|278 | |278 | ||
| − | |||
|adds environmental variables to last | |adds environmental variables to last | ||
|- | |- | ||
|lastz | |lastz | ||
|1.02.00 | |1.02.00 | ||
| − | |||
|adds environmental variables to lastz | |adds environmental variables to lastz | ||
|- | |- | ||
| − | |libstree | + | |[libstree http://www.icir.org/christian/libstree/] |
|0.4.2 | |0.4.2 | ||
| − | |||
|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. | |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 http://komarix.org/ac/lr/] |
|20060531 | |20060531 | ||
| − | |||
|LR-TRIRLS stands for Logistic Regression with Truncated Regularized Iteratively Re-weighted Least Squares. This is our contribution to LR computation. | |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 | |adds environmental variables to lua | ||
|- | |- | ||
| − | |MACS | + | |[MACS http://liulab.dfci.harvard.edu/MACS/] |
|1.4.2, 2.0.10 | |1.4.2, 2.0.10 | ||
| − | |||
|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. | |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 | |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 | |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 | |adds environmental variables to matlab | ||
|- | |- | ||
|mcl | |mcl | ||
|12-068 | |12-068 | ||
| − | |||
|adds environmental variables to orthomcl | |adds environmental variables to orthomcl | ||
|- | |- | ||
| − | |MEGAN | + | |[MEGAN http://ab.inf.uni-tuebingen.de/software/megan/] |
|4.70.4, 5.1.0 | |4.70.4, 5.1.0 | ||
| − | |||
|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. | |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 | |adds environmental variables to smrtanalysis-1.4.0 | ||
|- | |- | ||
|MetaGeneMark | |MetaGeneMark | ||
|2010 | |2010 | ||
| − | |||
|adds environmental variables to MetaGeneMark | |adds environmental variables to MetaGeneMark | ||
|- | |- | ||
|metAMOS | |metAMOS | ||
|1.2 | |1.2 | ||
| − | |||
|A metagenomic assembly pipeline for AMOS http://treangen.github.com/metAMOS/ | |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 | |adds environmental variables to MetaVelvet | ||
|- | |- | ||
|mfinder | |mfinder | ||
|1.2 | |1.2 | ||
| − | |||
|adds environmental variables to mfinder | |adds environmental variables to mfinder | ||
|- | |- | ||
|mira | |mira | ||
|3.2.1 | |3.2.1 | ||
| − | |||
|adds environmental variables to mira | |adds environmental variables to mira | ||
|- | |- | ||
|MOCAT | |MOCAT | ||
|1.1 | |1.1 | ||
| − | |||
|adds environmental variables for MOCAT | |adds environmental variables for MOCAT | ||
|- | |- | ||
|ModalClust | |ModalClust | ||
|0.2, 0.3 | |0.2, 0.3 | ||
| − | |||
|adds environmental variables to ModalClust | |adds environmental variables to ModalClust | ||
|- | |- | ||
| − | |mothur | + | |[mothur http://www.mothur.org/] |
|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 | ||
| − | |||
|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. | |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 http://www.mpich.org/] |
|3.0.4 | |3.0.4 | ||
| − | |||
|MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. | |MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. | ||
|- | |- | ||
| − | |mpich2 | + | |[mpich2 http://www.mpich.org/] |
|1.4.1p1, 1.5 | |1.4.1p1, 1.5 | ||
| − | |||
|MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. | |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 | |adds environmental variables to msort | ||
|- | |- | ||
|MUMmer | |MUMmer | ||
|3.23 | |3.23 | ||
| − | |||
|adds environmental variables to MUMmer | |adds environmental variables to MUMmer | ||
|- | |- | ||
|muscle | |muscle | ||
|3.8.31 | |3.8.31 | ||
| − | |||
|adds environmental variables to velvet | |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 | |adds environmental variables to novocraft | ||
|- | |- | ||
| − | |oasas-kmer245 | + | |[oasas-kmer245 http://www.ebi.ac.uk/~zerbino/oases/] |
|0.2.8 | |0.2.8 | ||
| − | |||
|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. | |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 http://www.ebi.ac.uk/~zerbino/oases/] |
|0.2.8 | |0.2.8 | ||
| − | |||
|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. | |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 | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
| − | |openmpi-intel | + | |[openmpi-intel http://www.open-mpi.org/] |
|1.6.3 | |1.6.3 | ||
| − | |||
|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. | |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 http://www.open-mpi.org/] |
|1.4.3, 1.6.3 | |1.4.3, 1.6.3 | ||
| − | |||
|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. | |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 | |adds environmental variables to orthomcl | ||
|- | |- | ||
|paml | |paml | ||
|4.4 | |4.4 | ||
| − | |||
|adds environmental variables to paml | |adds environmental variables to paml | ||
|- | |- | ||
|parallel | |parallel | ||
|20121122 | |20121122 | ||
| − | |||
|adds environmental variables to orthomcl | |adds environmental variables to orthomcl | ||
|- | |- | ||
|pathway-tools | |pathway-tools | ||
|16.5 | |16.5 | ||
| − | |||
|adds environmental variables to pathway-tools | |adds environmental variables to pathway-tools | ||
|- | |- | ||
|PBJelly | |PBJelly | ||
|12.9.14 | |12.9.14 | ||
| − | |||
|adds environmental variables to PBJelly with smrtanalysis-1.4.0 | |adds environmental variables to PBJelly with smrtanalysis-1.4.0 | ||
|- | |- | ||
|peaksplitter | |peaksplitter | ||
|1.0 | |1.0 | ||
| − | |||
|adds environmental variables to peaksplitter | |adds environmental variables to peaksplitter | ||
|- | |- | ||
|perfsuite | |perfsuite | ||
|1.0.0 | |1.0.0 | ||
| − | |||
|adds environmental variables to perfsuite | |adds environmental variables to perfsuite | ||
|- | |- | ||
| − | |perl | + | |[perl http://www.perl.org] |
|5.16.1 | |5.16.1 | ||
| − | |||
|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. | |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/ | |ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/ | ||
|- | |- | ||
|phred | |phred | ||
|0.020425.c | |0.020425.c | ||
| − | |||
|adds environmental variables to qiime and qiime | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|phylip | |phylip | ||
|3.69 | |3.69 | ||
| − | |||
|adds environmental variables to phylip | |adds environmental variables to phylip | ||
|- | |- | ||
|phymmbl | |phymmbl | ||
|4.0 | |4.0 | ||
| − | |||
|adds environmental variables to phymmbl | |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 | |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. | |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 | |adds environmental variables to pplacer | ||
|- | |- | ||
|prank | |prank | ||
|121002 | |121002 | ||
| − | |||
|adds environmental variables to prank | |adds environmental variables to prank | ||
|- | |- | ||
|prodigal | |prodigal | ||
|2.0, 2.2 | |2.0, 2.2 | ||
| − | |||
|adds environmental variables to prodigal | |adds environmental variables to prodigal | ||
|- | |- | ||
|python | |python | ||
|2.6.6, 2.7.3, 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 | |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, 1.8.0 |
| − | |||
|Loads qiimes environmental variables | |Loads qiimes environmental variables | ||
|- | |- | ||
| − | |quake | + | |[quake http://www.cbcb.umd.edu/software/quake/] |
|0.3.4 | |0.3.4 | ||
| − | |||
|Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. | |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 | |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 | |adds environmental variables for EFI QUEST development branch | ||
|- | |- | ||
| − | |R | + | |[R http://www.r-project.org/] |
|2.15.0, 2.15.1, 2.15.2, 3.0.0, 3.0.2 | |2.15.0, 2.15.1, 2.15.2, 3.0.0, 3.0.2 | ||
| − | |||
|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. | |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 http://sco.h-its.org/exelixis/software.html] |
|7.3.0 | |7.3.0 | ||
| − | |||
|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. | |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 | |Ray -- Parallel genome assemblies for parallel DNA sequencing denovoassembler.sourceforge.net/index.html | ||
|- | |- | ||
| − | |rdp_classifier | + | |[rdp_classifier http://rdp.cme.msu.edu/] |
|2.5 | |2.5 | ||
| − | |||
|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. | |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' | |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 | |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/ | |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 | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|rstudio | |rstudio | ||
|0.97.312 | |0.97.312 | ||
| − | |||
|adds environmental variables to R | |adds environmental variables to R | ||
|- | |- | ||
|ruby | |ruby | ||
|1.9.3 | |1.9.3 | ||
| − | |||
|adds environmental variables to ruby | |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/ | |http://sourceforge.net/projects/samtools/files/ | ||
|- | |- | ||
|sam_comp | |sam_comp | ||
|0.7 | |0.7 | ||
| − | |||
|adds environmental variables Python 2.7.3 | |adds environmental variables Python 2.7.3 | ||
|- | |- | ||
|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 | |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 | |adds environmental variables to perl | ||
|- | |- | ||
| − | |smrtanalysis | + | |[smrtanalysis http://pacbiodevnet.com/] |
|1.4.0, 2.0.1 | |1.4.0, 2.0.1 | ||
| − | |||
|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. | |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/ | |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 | |adds environmental variables to SOAP2 | ||
|- | |- | ||
| − | |SOAPdenovo-Trans | + | |[SOAPdenovo-Trans http://soap.genomics.org.cn/SOAPdenovo-Trans.html] |
|1.02 | |1.02 | ||
| − | |||
|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-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 | |adds environmental variables to SOAPdenovo | ||
|- | |- | ||
|SOAPdenovo2 | |SOAPdenovo2 | ||
|r240 | |r240 | ||
| − | |||
|adds environmental variables to SOAPdenovo2 | |adds environmental variables to SOAPdenovo2 | ||
|- | |- | ||
|SOAPec | |SOAPec | ||
|2.01, 2.02 | |2.01, 2.02 | ||
| − | |||
|http://soap.genomics.org.cn/about.html | |http://soap.genomics.org.cn/about.html | ||
|- | |- | ||
|SOAPErrorCorrection | |SOAPErrorCorrection | ||
|0.04 | |0.04 | ||
| − | |||
|adds environmental variables to SOAPErrorCorrection | |adds environmental variables to SOAPErrorCorrection | ||
|- | |- | ||
|SOAPGapCloser | |SOAPGapCloser | ||
|1.12 | |1.12 | ||
| − | |||
|adds environmental variables to SOAPGapCloser | |adds environmental variables to SOAPGapCloser | ||
|- | |- | ||
|SOAPprepare | |SOAPprepare | ||
|0.1 | |0.1 | ||
| − | |||
|adds environmental variables to SOAPdenovo | |adds environmental variables to SOAPdenovo | ||
|- | |- | ||
| − | |speciateit | + | |[speciateit http://sourceforge.net/p/speciateit/code/HEAD/tree/] |
|184 | |184 | ||
| − | |||
|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. | |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 http://sourceforge.net/p/speciateit/code/HEAD/tree/] |
|184 | |184 | ||
| − | |||
|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. | |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 | |adds environmental variables to sratoolkit | ||
|- | |- | ||
|srna-tools | |srna-tools | ||
|20130118 | |20130118 | ||
| − | |||
|adds environmental variables to srna-tools | |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 | |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 | |adds environmental variables to stacks | ||
|- | |- | ||
| − | |structure | + | |[structure http://pritch.bsd.uchicago.edu/structure.html] |
|2.3.4 | |2.3.4 | ||
| − | |||
|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. | |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/ | |Fast, accurate and scalable read mapping by seed-and-vote http://sourceforge.net/projects/subread/ | ||
|- | |- | ||
|supfam | |supfam | ||
|1.75 | |1.75 | ||
| − | |||
|produce SCOP protein domain assignments using the SUPERFAMILY hidden Markov models (HMMs) and associated scripts. | |produce SCOP protein domain assignments using the SUPERFAMILY hidden Markov models (HMMs) and associated scripts. | ||
|- | |- | ||
| − | |tabix | + | |[tabix http://samtools.sourceforge.net/tabix.shtml] |
|0.2.6 | |0.2.6 | ||
| − | |||
|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. | |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/ | |Description of the module http://www.tcoffee.org/ | ||
|- | |- | ||
|tmhmm | |tmhmm | ||
|2.0 | |2.0 | ||
| − | |||
|adds environmental variables to tmhmm | |adds environmental variables to tmhmm | ||
|- | |- | ||
|tophat | |tophat | ||
|1.4.1 | |1.4.1 | ||
| − | |||
|adds environmental variables to qiime and qiime | |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 | |2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10 | ||
| − | |||
|adds environmental variables to tophat 2 | |adds environmental variables to tophat 2 | ||
|- | |- | ||
| − | |treemix | + | |[treemix http://code.google.com/p/treemix/] |
|1.12 | |1.12 | ||
| − | |||
|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. | |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 | |adds environmental variables to trf | ||
|- | |- | ||
|trimmomatic | |trimmomatic | ||
|0.22, 0.27, 0.30 | |0.22, 0.27, 0.30 | ||
| − | |||
|adds environmental variables to trimmomatic | |adds environmental variables to trimmomatic | ||
|- | |- | ||
| − | |trinityrnaseq-intel | + | |[trinityrnaseq-intel http://trinityrnaseq.sourceforge.net/] |
|r2013-02-25 | |r2013-02-25 | ||
| − | |||
|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. | |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 http://trinityrnaseq.sourceforge.net/] |
|r2012-06-08, r2013-02-25, r2013-08-14 | |r2012-06-08, r2013-02-25, r2013-08-14 | ||
| − | |||
|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. | |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 | |Description of the module | ||
|- | |- | ||
| − | |truesight | + | |[truesight http://bioen-compbio.bioen.illinois.edu/TrueSight/] |
|0.06 | |0.06 | ||
| − | |||
|TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq. | |TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq. | ||
|- | |- | ||
|uchime | |uchime | ||
|4.2.40 | |4.2.40 | ||
| − | |||
|adds environmental variables to uchime | |adds environmental variables to uchime | ||
|- | |- | ||
| − | |usearch | + | |[usearch http://www.drive5.com/usearch/] |
|6.0.307, 6.1.544, 7.0.959 | |6.0.307, 6.1.544, 7.0.959 | ||
| − | |||
|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. | |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 | |adds environmental variables to USeq | ||
|- | |- | ||
| − | |vcftools | + | |[vcftools http://vcftools.sourceforge.net/index.html] |
|0.1.7, 0.1.11 | |0.1.7, 0.1.11 | ||
| − | |||
|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. | |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 http://www.ebi.ac.uk/~zerbino/velvet/] |
|1.2.10 | |1.2.10 | ||
| − | |||
|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 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 http://www.ebi.ac.uk/~zerbino/velvet/] |
|1.1.04, 1.2.08, 1.2.10 | |1.1.04, 1.2.08, 1.2.10 | ||
| − | |||
|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 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. | |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$ | |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 | |adds environmental variables to qiime and qiime | ||
|- | |- | ||
|wise | |wise | ||
|2.2.3-rc7 | |2.2.3-rc7 | ||
| − | |||
|adds environmental variables to wise | |adds environmental variables to wise | ||
|} | |} | ||
Revision as of 11:32, 17 February 2014
| Application | Installed Versions | Description |
|---|---|---|
| 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 http://sourceforge.net/apps/mediawiki/amos] | 3.1.0 | 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 | |
| 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 http://blast.ncbi.nlm.nih.gov/Blast.cgi] | 2.2.26 | 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 http://www.boost.org/] | 1.54 | Boost provides free peer-reviewed portable C++ source libraries. |
| [boost http://www.boost.org/] | 1.54 | Boost provides free peer-reviewed portable C++ source libraries. |
| [bowtie http://bowtie-bio.sourceforge.net] | 0.12.8, 0.12.9, 1.0.0 | 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 http://cdbfasta.sourceforge.net/] | 0.99 | 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 http://www.biostat.jhsph.edu/~hji/cisgenome/] | 2.0 | 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 http://cmpg.unibe.ch/software/fastsimcoal2/] | 1.1.1 | 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 http://www.broadinstitute.org/gatk] | 1.6-5, 1.6-13, 2.5-2, 2.6-4 | 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 http://genometools.org/] | 1.5.1 | 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 http://www.gnu.org/software/gsl/] | 1.16 | 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 http://hmmer.janelia.org/] | 2.3.2, 3.0 | 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 http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html] | 0.5.4 | 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 http://www.imagemagick.org] | 6.7.8-9 | 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 |
| 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 http://www.icir.org/christian/libstree/] | 0.4.2 | 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 http://komarix.org/ac/lr/] | 20060531 | 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 http://liulab.dfci.harvard.edu/MACS/] | 1.4.2, 2.0.10 | 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 http://ab.inf.uni-tuebingen.de/software/megan/] | 4.70.4, 5.1.0 | 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 http://www.mothur.org/] | 1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1 | 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 http://www.mpich.org/] | 3.0.4 | MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard. |
| [mpich2 http://www.mpich.org/] | 1.4.1p1, 1.5 | 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 http://www.ebi.ac.uk/~zerbino/oases/] | 0.2.8 | 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 http://www.ebi.ac.uk/~zerbino/oases/] | 0.2.8 | 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 http://www.open-mpi.org/] | 1.6.3 | 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 http://www.open-mpi.org/] | 1.4.3, 1.6.3 | 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 http://www.perl.org] | 5.16.1 | 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, 1.8.0 | Loads qiimes environmental variables |
| [quake http://www.cbcb.umd.edu/software/quake/] | 0.3.4 | 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 http://www.r-project.org/] | 2.15.0, 2.15.1, 2.15.2, 3.0.0, 3.0.2 | 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 http://sco.h-its.org/exelixis/software.html] | 7.3.0 | 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 http://rdp.cme.msu.edu/] | 2.5 | 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 |
| 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 http://pacbiodevnet.com/] | 1.4.0, 2.0.1 | 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 http://soap.genomics.org.cn/SOAPdenovo-Trans.html] | 1.02 | 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 http://sourceforge.net/p/speciateit/code/HEAD/tree/] | 184 | 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 http://sourceforge.net/p/speciateit/code/HEAD/tree/] | 184 | 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 http://pritch.bsd.uchicago.edu/structure.html] | 2.3.4 | 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/ |
| supfam | 1.75 | produce SCOP protein domain assignments using the SUPERFAMILY hidden Markov models (HMMs) and associated scripts. |
| [tabix http://samtools.sourceforge.net/tabix.shtml] | 0.2.6 | 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 http://code.google.com/p/treemix/] | 1.12 | 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 http://trinityrnaseq.sourceforge.net/] | r2013-02-25 | 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 http://trinityrnaseq.sourceforge.net/] | r2012-06-08, r2013-02-25, r2013-08-14 | 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 http://bioen-compbio.bioen.illinois.edu/TrueSight/] | 0.06 | TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq. |
| uchime | 4.2.40 | adds environmental variables to uchime |
| [usearch http://www.drive5.com/usearch/] | 6.0.307, 6.1.544, 7.0.959 | 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 http://vcftools.sourceforge.net/index.html] | 0.1.7, 0.1.11 | 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 http://www.ebi.ac.uk/~zerbino/velvet/] | 1.2.10 | 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 http://www.ebi.ac.uk/~zerbino/velvet/] | 1.1.04, 1.2.08, 1.2.10 | 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 |
