{AnyApplication} 1.0.0 true full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4 2016-02-02 true 100 tools.7z 25cfae9427660795286656384efdfb7d267d7f48 full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.20.1 2016-02-02 true 98 tools.7z 4ead7541f60bcc9e5bc855e8ecc05691eeec36ce full.tools.blast BLAST BLAST: Basic Local Alignment Search Tool (Old version). 2.2.26 2016-02-02 true 96 tools.7z cdbb76d8b88577de093e88a904805bd272d3f494 full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.2.30 2016-02-02 true 94 tools.7z 14c039738fdc142c5ddcf60e370bff85611309f4 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.0.0 2016-02-02 true 92 tools.7z 1dd3bd2ee4d79209ea5e51c674b73e5eb12ab86a 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 d6ccf52edbde39b8b93eeed042c5633f05a37b09 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 da3316227a0386d4b4edb6145e1c7f3978ceded7 full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07 2010-07-15 true 86 tools.7z 45bbacc9b532b30be662b43494825af4a807fc21 full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 tools.7z df99f61abec77fd789ac2f9ee042a6a30c6eb02b 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 0eec3ca4f0cfe261342594303e8e4ac01ec096ba 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 c375a1305b2c025e5a4afdc591bee903f83e6604 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 c0d73228a10000073968d987df1c94b0a71c7cdf 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 1a71e03365ab58a692b06375913f0fde66b0d960 full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.2 2016-02-02 true 76 tools.7z 1fb9de3eb1bb73c2ce42d674e0e8ef0d4e0fcc2e 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 da517a2835027d030103a29c12067eccdce985cb 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 820aeaa72a166ac4e903a6496f9759fd86e72930 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 tools.7z 27e4eff5dd641b8df410e6a22e0b27bafc40816c 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 36c1a3027b1286aa007b020f84cc976bfd359903 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 e843b72f88de02f1c65953f13dab295a0454321c 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 c9125e8000c1330afcffdfc9a8c1a2730f57a8ef 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 4528e9ca83b756dd03799b393bfb0ef5317b8fdc 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 a01213bf93be49097be54f2c3311f7231002c651 full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 tools.7z ddda7253835bacaa7d34a552a4462b61b2f98a27 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00 2016-02-02 true 58 tools.7z 25a0633e7c074227ae4fad2ae67999663c49e090 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 0844fe36e9bff0348578d700a675f9d96ae09e9e 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 d70a5d6bfda2fbec2972beb3aec986027e9900b1 NGS NGS package additions NGS extra data. 1.0.0 2016-02-02 80 435701c69bf5990a7832acdfa130fbd41ed4d3a0 NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 c1a84cdeb64dc632429ab46e0e7e42a8fe3155e3 NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2 2013-09-25 4293871bcafbe5613482e19ff70dbec59cfc25ba 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 22567e7eedb116c03325252f1ed35c12bcb4d4a1 full Full package additions Full package additions. 1.29.0 2017-12-29 90 true 67614e52d2fc7ae6e97a30d5baa2f13a372dd90b full.tools External tools External tools. 1.29.0 2017-12-29 90 true 9f91d02b89525a3a71234ee06b790aad0cf9b99d ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.29.0 2017-12-29 100 d78f26dc0df07b03565faa02e94de3648f2534cc ugene.data Data folder Data folder with examples of various data. true 1.29.0 ugene 2017-12-29 100 true data.7z c39c5a09eb0fadd0b9134a17e2382b12bb186329 ugene.ugene UGENE executables UGENE executables. true true 1.29.0 2017-12-29 100 imageformats.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z ac9b97283b2fb5759a41d5e9cd98f0bbd464902e