{AnyApplication} 1.0.0 true full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4 2016-02-02 true 100 tools.7z e5f10ccc3b40bc5ec4ee5ab27090cd54d6385aaa full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.20.1 2016-02-02 true 98 tools.7z 63a568f1738c1a73640829b63a44fb2ce4012282 full.tools.blast BLAST BLAST: Basic Local Alignment Search Tool (Old version). 2.2.26 2016-02-02 true 96 tools.7z a53e4567ea54c21f214592b80af947d6940deaf3 full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.2.30 2016-02-02 true 94 tools.7z 2714d3b963b7c7944d135128fc1b524f0b2978b9 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.0.0 2016-02-02 true 92 tools.7z 64640aab25df9118f0f1b9ad79cccecf2e064497 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 9603054be113b3c9947abe06d5f4ce37b273792e full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07 2010-07-15 true 86 tools.7z 95b4a00a77ddcc619bbc96a9bae2c36297f463b1 full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 tools.7z fdfe089bb561528fea6c4c9701772990e908f019 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 5864d26d499bc25d1026ea0f944b8cd917d5c1cf 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 329c08bddeeebc9c30dd196b7f4b8dfa63ad3698 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 314521ce1c8de2d15c9bd340735cce1b73710acb 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 77b78110d481bcb336d70eb7839d0cbe4cf88c34 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 521458a95be69ce017383e44ba7f1316e024c849 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 eb2e7693c9383fa66cda59084674c6991e44a019 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 tools.7z bf59715e4b9b65ca1ba4b3296c1321afe4bccdf5 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 e005b825f26e71344e34465b61b39d061b39eb69 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 d110176f642a4749d065557e447d15e38cf1dd26 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 a940c37e6b3aa513c7d9fb31094f4d38c54391ad 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 31262e8cb5c53513827758d1275af97286a42468 full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 tools.7z dc89666703760f049827232cb3291a7d3366b775 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00 2016-02-02 true 58 tools.7z fff42a0012ee0e5329232301843f59db0b1b46f5 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 00d702d85db7aebaf08979ea84f576386541770a 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 422c168892c979bf26da0329b0591a59450feb3e NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 46332bb857c3c5733851b49d49c4c34f479dce8f NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2 2013-09-25 15d0796e3c426007a0984d422a486ca79cc1bbb0 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 2e803a9c91138866919ea842adeef13f17ef69af full Full package additions Full package additions. 1.29.0 2017-12-29 90 true 0d455227c6958f51d62c88f8547fba5e92a8ced1 full.tools External tools External tools. 1.29.0 2017-12-29 90 true fc36e5bb340b2b0ede6065de49b53e96ad3028ba ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.29.0 2017-12-29 100 585b709236eb8f0f1db557a1ab912f18f15be450 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 aa20b80efbf70f1c6a2965ab4bca3bd2736f368f 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). 4.3.7 2016-12-16 true 64 tools.7z e4209614e4457678af3618b72bfe4286bcd67fec 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 f4b215d36b6d5d47dbfe85aa8bc169c0b1611294 full.tools.trimmomatic Trimmomatic Trimmomatic is a flexible read trimming tool for Illumina NGS data. 0.38 2015-03-10 true 79 tools.7z a584b35e5f0f4428584132ad17c1e2091463fb8f full.tools.bowtie2 Bowtie2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. 2.1.0.1 2016-02-02 true 90 full.tools.python,full.tools.perl tools.7z 1618c1603105c47c79b503e22cc77c15595204ef 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 2018-07-10 true 74 tools.7z 7af95102cb15524ceb0ed2d55b38c3c3f10e5ebf full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.8 2018-10-04 true 76 tools.7z 2789a274c830a1564aeb8edf9f5a6b1a37bdab32 ugene.data Data folder Data folder with examples of various data. true 33.0 ugene 2019.09.27 100 true data.7z 2c62d3561e8398d929240abc79de78e8962545a9 ugene.ugene UGENE executables UGENE executables. true true 33.0 2019.09.27 100 imageformats.7z,man1.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z 13d20c80790ef75302a6706e2ecb996db082066c