{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.
1.28.0
2017-10-26
90
true
095018ba4f8b05e52fbd7d0289c25bb33ff6e09a
full.tools
External tools
External tools.
1.28.0
2017-10-26
90
true
tools.7z
cb0019a343c8f402a0a8277de4965350b5ead885
ugene
Standard package
Standard package contains executables and data of Unipro UGENE.
true
true
1.28.0
2017-10-26
100
40b27d47dfe5e8d7de9f572f77bad30e8c3275de
ugene.data
Data folder
Data folder with examples of various data.
true
1.28.0
ugene
2017-10-26
100
true
data.7z
c37a36e945ad91b887e5bee21d81c2ecdf093904
ugene.ugene
UGENE executables
UGENE executables.
true
true
1.28.0
2017-10-26
100
imageformats.7z,man1.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z
b9fc2c35aff5d2cd161bf87bdf5007f978191ae0