{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.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 0474c9e5d06e024552f344cfd85989af68067f03 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 NGS package additions NGS extra data. 1.0.0 2016-02-02 80 459df0b44ea75d02ec6b0144836b1e3dba344d3d 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 ugene.data Data folder Data folder with examples of various data. true 1.30.0 ugene 2018-05-31 100 true data.7z bc13581862409619602f0d086e463a4e0b0a5a82 ugene.ugene UGENE executables UGENE executables. true true 1.30.0 2018-05-31 100 imageformats.7z,man1.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z e452ac827f00a31e72e4c8656d37fc842b0825a0 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