{AnyApplication} 1.0.0 true full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4 2016-02-02 true 100 tools.7z 0e5322232a3ef6dea113dc4b689f868185194dca full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.20.1 2016-02-02 true 98 tools.7z aec2a53c6746f92b6825aaf7e340e49b96d5d6b6 full.tools.blast BLAST BLAST: Basic Local Alignment Search Tool (Old version). 2.2.26 2016-02-02 true 96 tools.7z 1895d1f198fc84d2da1af73cf04db915d6a9beb7 full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.2.30 2016-02-02 true 94 tools.7z cc9ae7655570af08690f388cddd21dc73f525ffd full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.0.0 2016-02-02 true 92 tools.7z 3dff266a9d4a780c78ba2464e2cb9584dedc82e8 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 9166314007f9b0259cb3f35914599d02069bbc81 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 648b62ae60839b073aff1abae6f17ad3c4228d13 full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07 2010-07-15 true 86 tools.7z 02108268980bda583ca829420047755a8680a81e full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 tools.7z 586931ad2ec5df6d98cffc721cc3d918111f1aab 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 87a69ba8363f590b76091a924a45c3c0925468a1 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 708816418ae26719e6014118171928458c216bc5 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 9deaeea41ee243675002663e8af0d470edb55553 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 4a576618c6f915728d6997b4edb4a6ef0669a1d0 full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.2 2016-02-02 true 76 tools.7z 280ca21379bc25090e0d817f305e52d661f8dd76 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 8d1aa91f4ab48abf89b0c60dbd5c89e809023b0b 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 5fc1e2fe7ae8bc91ec276085ca649b65111ce220 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 tools.7z cd70c373dfc8f9e824dcaa615b7bf2f6bac76b9a 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 4f8ed7c783bb253a30a58b948dfd641a47cb77e8 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 9fac6727e1dbafcd5752c4cdee6d319b94c376e7 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 79e29860266339cdb07340452d4f3852e21f1f6d 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 054134bb89913a3f24d6d437fd50717a0147468d full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 tools.7z 247c545f43b68682fbd8ccaff343634236bb4bd0 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00 2016-02-02 true 58 tools.7z 8d0686cd0ef66eea3aa5146a5a0f8f27fb4dc53f 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 1929d3216d6714bed2ce20da795e2ec8f90d40a2 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 9e9027d771c66865722e58aa2c763f3cf10fda95 NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 data.7z 7eadbe8215ac6a09a591443c89b23d47ad2ac97a NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2 2013-09-25 tools.7z cf7d62e7ca47a1c8f59fe01c7d5ed08c3119873e 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). 3.1 2015-05-05 true 75 tools.7z 4fbf6b8f39e8feafdffd04dfb78da5c63e435510 full Full package additions Full package additions. 1.29.0 2017-12-29 90 true c3ad421b2968ee65c661b9f53aaeb2be5c4d5575 full.tools External tools External tools. 1.29.0 2017-12-29 90 true a75e4989a3031bf7aa06f10f9876ecdb2de80e99 ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.29.0 2017-12-29 100 9ce3e1826bd3085aa7fc6b7a5bd964bbcf6d6e3d 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 f259fa9342975e25a3b22010389e936d8de97571 full.tools.stringtie StringTie StringTie is an assembler of RNA-Seq alignments into potential transcripts. 1.3.4.4 2018-02-25 true 80 tools.7z a54e76b3499afce00b655ac120377442d3433447 full.tools.trimmomatic Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. 0.38 2015-03-10 true 79 tools.7z b601137b3d45f772bdde02ca7cbe2531c4f003a4 ngs_classification.wevote.tools WEVOTE external tools Check this component to install WEVOTE executables. ngs_classification.taxonomy 1.0.0 2018-01-29 100 tools.7z 2ac3617b2eef014e7d5f5eed3cd8274bdeef3574 full.tools.SPAdes SPAdes SPAdes is intended for both standard isolates and single-cell MDA bacteria assemblies. 3.12.0 2018-05-14 false 62 tools.7z a257b4d072d3fd96bf5bd75eda6a109b87db3c77 ngs_classification.refseq RefSeq reference data Check this component to download NCBI RefSeq bacterial, viral and human data. The data can be used to build a database for CLARK. To build a database for Kraken unpack the data first. 1.0.0 2018-08-06 90 c6b76007fa7088256e2844543f9d5a6c8a8501af 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 3c91af0bbe9df613009cd9b883e7abb68828e0a6 ngs_classification NGS additions: metagenomics classification The component contains external tools and reference data for taxonomy classification of metagenomic whole-genome shotgun sequencing data. 1.0.0 2017-12-08 85 a4a34ed770d047aec294155680756a9a5242c946 ngs_classification.clark.tools CLARK external tools Check this component to install CLARK executables. ngs_classification.taxonomy 1.2.4.1 2018-08-02 100 tools.7z 89908422b997486acdc7ca725b4edfa64cb19be3 ngs_classification.diamond.tools DIAMOND external tools Check this component to install DIAMOND executables. ngs_classification.taxonomy 0.9.22 2018-05-11 100 tools.7z 9a1047c4f7c92c3f397451b20982b80d4f1bf443 ngs_classification.kraken.tools Kraken external tools Check this component to install Kraken executables. ngs_classification.taxonomy 1.0.0 2017-10-20 100 tools.7z 79d48ca15d674f487214370230db228fb9f90c35 ngs_classification.clark Classification with CLARK CLARK (CLAssifier based on Reduced K-mers) is a tool for taxonomy classification of metagenomic NGS data. Databases with viral and viral+bacterial NCBI RefSeq data are provided by default for CLARK-l variant of the tool launched with default parameters. One can also build a custom database. 1.31.0 2018-08-17 70 324fc963113967e9a671b2fcabfa8cb4c289a52d ngs_classification.diamond Classification with DIAMOND In general, DIAMOND is a sequence aligner for protein and translated DNA searches similar to NCBI BLAST, but much faster. In UGENE it is integrated for taxonomy classification of metagenomic NGS data. Reference databases UniRef50 and UniRef90 are provided by default. One can also build a custom database. 1.31.0 2018-08-17 65 0f53ebb8fb0d2f00f85d9b46fb280c49a9b6e005 ngs_classification.kraken Classification with Kraken Kraken is a tool for taxonomy classification of metagenomic NGS data. A MiniKraken reference database is provided by default with the tool. One can also build a custom database. 1.31.0 2018-08-17 80 f56fe5394f25c5ce30a80353563bc97c003e4d93 ngs_classification.wevote Classification with WEVOTE WEVOTE (WEighted VOting Taxonomic idEntification) is a tool for taxonomy classification of metagenomic NGS data, based on an ensemble of other classification methods (Kraken, CLARK, etc.). 1.31.0 2018-08-17 60 e4234512bced1d1ff7a1e30aacd7c19fc5b1f287 ugene.data Data folder Data folder with examples of various data. true 1.31.0 ugene 2018-08-17 100 true data.7z b61af88fc3cb9cf22bfef97deb0d6f04467c7dc7 ugene.ugene UGENE executables UGENE executables. true true 1.31.0 2018-08-17 100 imageformats.7z,man1.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z ebfef3e638b2de25b8a8db2c188ecc80b5f72408