{AnyApplication} 1.0.0 true full.tools.bedGraphToBigWig bedGraphToBigWig Convert a bedGraph file to bigWig format. 4 2016-02-02 true 100 Contents.7z 52650db425bdccdeab3cc8b6b2952f878b438dd8 full.tools.bedtools2 BEDtools Flexible tools for genome arithmetic and DNA sequence analysis. 2.20.1 2016-02-02 true 98 Contents.7z bd154ddd184e179ac719c27b4663d37eadfc2fec full.tools.blast BLAST BLAST: Basic Local Alignment Search Tool (Old version). 2.2.26 2016-02-02 true 96 Contents.7z e1e5df326f0e9d07a457e646f3c10d147f896f11 full.tools.blast+ BLAST+ BLAST+: Basic Local Alignment Search Tool. 2.2.30 2016-02-02 true 94 Contents.7z fc93e3b788f0e4b0d0fce930637d7e9cba361e67 full.tools.bowtie Bowtie Bowtie is an ultrafast, memory-efficient short read aligner. 1.0.0 2016-02-02 true 92 Contents.7z 60276613ed2c1e285f091d982434f8fd070ad2ae 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 Contents.7z 7d6c452dfebddfeb90549e75604778f8812ebf3e 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 Contents.7z 7d36468c1c88c6f97c801c77209ac5374b10a63a full.tools.CAP3 CAP3 CAP3 Sequence Assembly Program. 10-15-07 2010-07-15 true 86 Contents.7z 967904b8393bdd3eae0b67a8464f35083ede31c1 full.tools.cistrome Cistrome External tools for the Cistrome workflow. 2.0.8 2016-02-02 true 56 Contents.7z 8e7c8194a27c1685a2c788f55f65c53d93ae6ee1 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 Contents.7z 6a2956453dbeb31648f95e2e0e605c43874f67ff 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 Contents.7z e9439e788d38bfa177d2c7b18918735dd63c777a 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 Contents.7z 770bc1965d51fdcefeebd4a8e96c727f7e805899 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 Contents.7z 3d9d0f1ee8ab0778d196b7558b50b5a5c5210d00 full.tools.fastqc FastQC FastQC - A high throughput sequence QC analysis tool. 0.11.2 2016-02-02 true 76 Contents.7z ecdb6a8cc431f5dbb714c968492f9e61232ff28d 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 Contents.7z 195930a899e8ed17b349d730b2ee6da1ebf909e2 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 Contents.7z 5c12d5c26fc0754e0e0b0373e6f12b6558f2d29c 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 Contents.7z 0fae0937f3727a6ffbfd9f53d124a36ba83f2332 full.tools.perl Perl Perl is a highly capable, feature-rich programming language. 5.10.0.5 2013-06-24 true 68 b561347243c1db592f96a584d32147b8646bd498 full.tools.phyml PhyML A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. 20120412 2012-04-12 true 70 Contents.7z 11f669dd70a0227e52a9cdd25bf2f17a16001c5d full.tools.python Python Python is a widely used general-purpose, high-level programming language. 2.7.5 2016-02-02 true 68 Contents.7z 1ac6a7640e0471e13d5b694cf574b9ba2faed807 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. 0.1.19-1 2016-02-02 true 66 Contents.7z 451e264c8780000891cd0927950282afaeec0053 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 2016-12-15 true 64 Contents.7z 1be723f030bf0e6902c2e43eff978b7f0df0dfc5 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 Contents.7z 83beff68744cfaa963399471e20416a8bdb9bb6d full.tools.spidey Spidey Spidey is an mRNA-to-genomic alignment program. 1 2016-02-02 true 60 c540cb8056b04aed47a10441e8b9f0038e8d1625 full.tools.tcoffee T-COFFEE T-Coffee is a multiple sequence alignment package. 11.00 2016-02-02 true 58 Contents.7z eb27c9269becdf791960012bec8d7cee599c38bc 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 Contents.7z 5b351a12d853902e97ec0f4f546e6d905850a5bb 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 Contents.7z 13acfaf56ed8c62cb450f6bdf085e572779caf77 NGS NGS package additions NGS extra data. 1.0.0 2016-02-02 80 20175dfcc5a5b5588438e56dec9a148a45e2a31e NGS.cistrome Data for the Cistrome workflow (for ChIP-Seq) Sample data for the Cistrome workflow. 1.0.0 2010-07-15 Contents.7z 2ac8ad766526504304bfc2ec0947a28680d4de00 NGS.RScript RScript external tool RScript is an alternative front end for use R scripts. 3.0.2 2013-09-25 Contents.7z 418ad3ad3573bccf3619df41b2c1246967a1ee24 full Full package additions Full package additions. 1.28.1 2017-11-21 90 true 65c7f164ee7982664793d7464fcab431f8bc7253 full.tools External tools External tools. 1.28.1 2017-11-21 90 true 60c7632753a5d1f34cd07d38282482174afe80e3 ugene Standard package Standard package contains executables and data of Unipro UGENE. true true 1.28.1 2017-11-21 100 4a629deb355f4b592ea239519ff2e40f4ab408ee ugene.data Data folder Data folder with examples of various data. true 1.28.1 ugene 2017-11-21 100 true Contents.7z b381d3b0ba74b7a7754ac601332f080461d5e250 ugene.ugene UGENE executables UGENE executables. true true 1.28.1 2017-11-21 100 Contents.7z 7357ea25643d0483a9064d2c1d32a6f3f4a0e722