{AnyApplication} 1.0.0 true full Full package additions Full package additions. 1.23.0 2016-02-02 90 true 873ac36b6ebaede9810149f4e74c619d15ccb080 full.tools External tools External tools. 1.23.0 2016-02-02 90 true tools.7z 4eb4b86dfbc0553f4735634f688abba374e8937a full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4 2016-02-02 true 100 tools.7z 557dbee115fa49f63f2a21ca643d6407ded197e5 full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.20.1 2016-02-02 true 98 tools.7z d304e57cbb35f919a3a5f33ed108d38d919e18d9 full.tools.blast BLAST BLAST: Basic Local Alignment Search Tool (Old version). 2.2.26 2016-02-02 true 96 tools.7z b04aab57b0a899035f4003e34fb9bd5e7ad3a861 full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.2.30 2016-02-02 true 94 tools.7z 857fbb22abd6a6092df6bf055aca32304984fb65 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.0.0 2016-02-02 true 92 tools.7z 3358dfe6573d0b8bb3412e5856f090448c488714 full.tools.bowtie2 Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 2.1.0 2016-02-02 true 90 tools.7z 882d54278c46131a95cb7395420babb19d2ccd50 full.tools.bwa BWA Burrows-Wheeler Aligner is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. 0.7.12 2016-02-02 true 88 tools.7z 3b65d0a12ec00b0c3b10f638495806e33f8f0f3d full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07 2010-07-15 true 86 tools.7z 2f79bd986d036ad6427aae2691048e7c3db88e06 full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 tools.7z 36f1116f639ae15d7d473b22656d4b82484f173a full.tools.clustalo ClustalO 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. 1.2.1 2014-12-08 true 84 tools.7z 3a3cd6d4ce75f51ffbac0f6f1bca75179a6bcc7e full.tools.clustalw ClustalW2 ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. 2.1 2016-02-02 true 82 tools.7z 47875b5362c7c5be3daa28645eb4cddd539cf3dc full.tools.cufflinks Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. 2.0.2 2016-02-02 true 80 tools.7z 70d31e949ddc11b35b397b809c8ecebf71c20ffa full.tools.cutadapt Cutadapt Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. 1.7.1 2016-02-02 true 78 full.tools.python tools.7z c3503211ef8e271c707b6748dbcafa714098c66c full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.2 2016-02-02 true 76 tools.7z 6faccd00525e193ea89dd01ebea26a9536b097a8 full.tools.mafft MAFFT MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. 7.212 2014-11-21 true 74 tools.7z 51ac87f46847b653a71ae0c3ae7ea97896442809 full.tools.mrbayes MrBayes MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. 3.2.3 2016-02-02 true 72 tools.7z be51ef6804b2ecd60d7193a99dddeb489c2ed919 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 tools.7z 88d0f1c249c1072efa3de98bb52d14f7618c48bc full.tools.phyml PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. 20120412 2012-04-12 true 70 tools.7z f20edb31066428c519e3294f10490dd685af5b49 full.tools.python Python Python is a widely used general-purpose, high-level programming language. 2.7.5 2016-02-02 true 68 tools.7z 7c0a933c568e61878d3fb3131904af67303432e6 full.tools.samtools SAMtools SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. 0.1.19 2016-02-02 true 66 tools.7z 67883c39be1f755982fe52c61c5c71ede9eb80ce full.tools.snpEff SnpEff Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). 4.1 2016-02-02 true 64 tools.7z 426688127191a84c6eb18f833c42853f9cbfc46f full.tools.SPAdes SPAdes SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. 3.6.0 2015-08-17 false 62 tools.7z 0a868619d587796a108400400be3ce20a40f7fe4 full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 tools.7z 81988611ef7f247e7e4f0c24d0a11bf3f698c0e1 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00 2016-02-02 true 58 tools.7z fe5d85faf7dd8da3a08fde1a755819973654b1ce full.tools.tophat TopHat TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. 2.0.8 2016-02-02 true 56 tools.7z 623a2e6539bad8a78516bc74efd92399f0c2c6ad full.tools.vcftools VCFtools VCFtools is 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 easily accessible methods for working with complex genetic variation data in the form of VCF files. 0.1.12 2016-02-02 true 54 tools.7z 5ee8be27dabb784747499340ec4c4a58b375e197 NGS NGS package additions NGS extra data. 1.0.0 2016-02-02 80 d7a77dd3cca1cbde80c871b6be660fdc0b3019b5 NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 data.7z e868412e02a1d5e781798d590aec2efe0d8a35ad NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2 2013-09-25 tools.7z fa76481ab84ef60a1349f814c62ff5cbd8633c3b ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.23.0 2016-05-12 100 b257bd4b9b1a4b96e7dea5d74a306fd896d713ac full.tools.hmmer HMMER HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. 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