{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.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
81a8034686afb8e815fd56ef9a95232cb52778c1
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.fastqc
FastQC
FastQC - A high throughput sequence QC analysis tool.
0.11.2
2016-02-02
true
76
tools.7z
e1e1da37a15b80a8a52618780e51fc0e71e33230
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.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
55cf255de2f5d6f35645193f84e71513f7ec7023
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
NGS package additions
NGS extra data.
1.0.0
2016-02-02
80
6f1ae38e04aa4a8e3c865b33ea1a83f348edc9b7
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.
1.28.0
2017-10-26
90
true
933075b02684de3a4ef34a0ba096e5a700ff7368
full.tools
External tools
External tools.
1.28.0
2017-10-26
90
true
tools.7z
f44ebb5913bbb957c4eb1764d3d88d34a2e078dd
ugene
Standard package
Standard package contains executables and data of Unipro UGENE.
true
true
1.28.0
2017-10-26
100
1c7f420429aa2dae86165af089fc8ac2cb7de641
ugene.data
Data folder
Data folder with examples of various data.
true
1.28.0
ugene
2017-10-26
100
true
data.7z
cdd4df4dcfd8db67a03ee54061cfe9e3ca99e120
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
2c5e503d706be0204376db54d10fa21789ef9337