{AnyApplication} 1.0.0 true full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 tools.7z 36f1116f639ae15d7d473b22656d4b82484f173a 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.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.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 NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 1 data.7z e868412e02a1d5e781798d590aec2efe0d8a35ad full Full package additions Full package additions. 1.29.0 2017-12-29 90 true 2c00243b89e27ef3a497b82787bf2f7a4c1af3bf full.tools External tools External tools. 1.29.0 2017-12-29 90 true 3daf6575d26d06dcabb16c0df9f14a3dbaa5b401 installer UGENE Maintenance Tool An installation and update tool for Unipro UGENE. true true true 3.0.3.1 2018-05-31 100 content.7z 6eef428b3efcfe3c500fd8073004930a321458f7 NGS NGS additions: ChIP-Seq data analysis The component contains external tools and reference data, required to analyze ChIP-Seq data with the Cistrome workflow. 1.0.0 2016-02-02 80 791a0f92b965acca972859320bb484c8329b875b NGS.cistromeTool Cistrome External tools for the Cistrome workflow. 2.0.8.1 2020-03-18 2 full.tools.cistrome NGS.RScript tools.7z 29ab3e478915d6af6f50ef16c5baa1d3ed56fdef ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 34.0.1 2020-05-15 100 73d75b81559d03f9fa7a829c3903f6b8a5715c9f full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.29.2 2019-12-18 true 98 tools.7z 770c037b9890645aa2b1e1110ff014d3384fb4a8 full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.10.1 2020-06-08 true 94 tools.7z 068b07f84361cdd805d0d9c66cd80923e3187106 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.3.0 2020-07-22 true 92 tools.7z d1832ad91d255a0403eb2a544d76d28b37eed0cc full.tools.bowtie2 Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 2.4.2 2020-05-10 true 90 full.tools.python,full.tools.perl tools.7z c7d025e02b44d8817c53d3577d9573babc6caf85 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. 0.7.17 2017-11-07 true 88 tools.7z aa3deab3d4579219550c2625846bf59f240e34bb full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.9 2019-01-08 true 76 tools.7z 1532bf12a118bb50eb2f601f468b65fe88adc7db full.tools.hmmer HMMER HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). 3.3.1 2020-07-25 true 75 tools.7z 39c3cd60c52c20a39215b464586ee30f5ee93b31 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. 7.475 2020-11-26 true 73 tools.7z 4c011d076b9f44b8b8b74eb5a64ec88dec62c1ae full.tools.trimmomatic Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. 0.39 2019-04-08 true 79 tools.7z 6c566f6cdc881313587e55238f682b95ad6f5b9e full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4.0.0.0.1 2016-02-02 true 100 tools.7z fed3144fa5cdfd001360ed21d51c615dbbf77a50 full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 12-21-07-1 2007-12-21 true 86 tools.7z 4e525cd90fd489f72b0b3c28d28d74d910d64ca5 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. 1.2.2.0.1 2016-07-01 true 84 tools.7z f95613240f47672fbc22b3c41d5de8c54d94ee83 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. 1.7.1.0.1 2014-11-25 true 78 full.tools.python tools.7z 17d5c0d4cd2f01558c0b978a63b7cb538958d190 full.tools.java Java "java" (JRE, Java Runtime Environment) is required to run several other external tools (e.g. FastQC and Trimmomatic). 1.8.0.192.1 2018-10-16 true 74 tools.7z a9407d39732fd5c480057d89e8bab6538d410450 full.tools.mrbayes MrBayes MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. 3.2.3.0.1 2014-10-22 true 72 tools.7z 1efbc01eeb5d3bc5d478773899dc2190d9f645d8 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.24.3.0.1 2017-09-22 true 68 tools.7z 2a64131c0ce40315f534f94f8d46dd8fa5ff0681 full.tools.phyml PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. 20120412.0.0.0.1 2012-04-12 true 70 tools.7z 0070dacd45d05833d44e2330f1968efefce1cec3 full.tools.python Python Python is a widely used general-purpose, high-level programming language. 2.7.5.2 2013-05-15 true 68 tools.7z 58c4a73d8be7a3a0b45107668e39395d8a4ff85d 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. 0.1.19.0.1 2013-03-19 true 66 tools.7z 59a70f68e42de8c4e09ea96de743f73c82cea003 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). 4.3.8.0.1 2016-12-16 true 64 tools.7z dc69ca9cf1567018af668ba0afef3c1bb0186963 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00.0.0.1 2014-08-12 true 58 tools.7z 09ef2152c7926539e8661652bd2c138f4dff4560 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. 0.1.12.2.1 2014-08-04 true 54 tools.7z b8d77c90f0b5ac7f6ea6cc0a6fdb478df5c54a08 full.tools.clustalw ClustalW2 ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. 2.1.0.0.1 2010-11-17 true 82 tools.7z b175342798b3c20d6e4d3699d9858a5e2d745369 NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2.0.1 2013-09-25 3 tools.7z 821691b2de568c7a3f2b633ef2fb75688aa4033a ugene.data Data folder Data folder with examples of various data. true 38.1 ugene 2021-03-26 100 true data.7z 6ce0d8477ad30fa67a1c0779b66c9ab36164aa33 ugene.ugene UGENE executables UGENE executables. true true 38.1 2021-03-26 100 imageformats.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z 345e38fbfc0ede9f9148d2fac4808b2c7be1f2e1