{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