{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.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.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.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.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
installer
UGENE Maintenance Tool
An installation and update tool for Unipro UGENE.
true
true
true
3.0.3.1
2018-05-31
100
content.7z
210bf195ed902498763c1bde73251a9ab2122c71
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).
4.3.7
2016-12-16
true
64
tools.7z
c4dc0895994d9fb11fd06085190bf2a9497865ee
NGS
NGS additions: ChIP-Seq data analysis
The component contains external tools and reference data, required to analyze ChIP-Seq data with the Cistrome workflow.
1.0.0
2016-02-02
80
0d825cae9f6b4dcb10bb80a5a3ed2d96362d301e
full.tools.trimmomatic
Trimmomatic
Trimmomatic is a flexible read trimming tool for Illumina NGS data.
0.38
2015-03-10
true
79
tools.7z
b3f4809a15fd326a49311b18faaf64f798d9ea47
full.tools.bowtie2
Bowtie2
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
full.tools.python,full.tools.perl
2.1.0.1
2016-02-02
true
90
tools.7z
f82f7a36df8215c8a8e6891254c86326c9674dcc
full.tools.perl
Perl
Perl is a highly capable, feature-rich programming language.
5.24.0
2016-05-09
true
68
tools.7z
a103f5a61d90180e9f6b29be3b3edcd43d4506d1
full.tools.java
Java
"java" (JRE, Java Runtime Environment) is required to run several other external tools (e.g. FastQC and Trimmomatic).
1.8.0
2018-07-10
true
74
tools.7z
7fd821819fda59d83fb16e359889e45399bdf63b
ugene.data
Data folder
Data folder with examples of various data.
true
1.32.0
ugene
2019.02.27
100
true
data.7z
ca492fb51b2af49b6213c70eedfbcbece85ecd52
ugene.ugene
UGENE executables
UGENE executables.
true
true
1.32.0
2019.02.27
100
imageformats.7z,platforms.7z,plugins.7z,sqldrivers.7z,content.7z
7bd7b698a4416d9d898fe1819f11d847e0f62ce5