Unipro UGENE Online User Manual v. 33
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changes.mady.by.user Olga Golosova

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  • Embedded tool: the tool is integrated into the UGENE source code. Such tools are always available in UGENE independently on the UGENE package type and operating system. 
  • External tool:
    • Integrated (supported) external tool: the tool executable file (or files) is provided with UGENE. It is launched when one uses the tool in the UGENE GUI. The result is also shown in the UGENE GUI. Note that the tool may be available on some operating systems only.
    • Custom external tool: it is possible to add any custom external tools tool as a workflow element in the Workflow Designer. See "Custom External Tools" documentation chapter for details.

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JRE is not included into the External Tools Packages.2.0.0
External toolWindows (64-bit)Windows (32-bit)macOS (64-bit)Linux (64-bit)Linux (32-bit)
bedGraphToBigWig4N/A44N/A
bedtools2.20.12.20.12.20.12.20.12.20.1
BLAST2.2.262.2.262.2.262.2.262.2.26
BLAST+2.2.302.2.302.2.302.2.302.2.30
Bowtie0.12.70.12.71.0.01.0.01.0.0
Bowtie22.3.14.032.1.0.62.3.14.032.13.4.032.1.0
BWA0.7.120.7.120.7.120.7.120.7.12
CAP312/21/0712/21/07

12/21/07

12/21/0712/21/07
CEAS1.0.21.0.21.0.21.0.2N/A

CLARK

N/AN/A1.2.4 (UGENE-customized)1.2.4 (UGENE-customized)N/A
ClustalO1.2.11.2.11.2.11.2.11.2.1
ClustalW2.12.12.12.12.1
ConductGOVersion not specifiedVersion not specifiedVersion not specifiedVersion not specifiedN/A
conservation_plot0.1.00.1.00.1.00.1.0N/A
Cufflinks toolsN/AN/A2.0.22.0.2N/A
Cutadapt1.7.11.7.11.7.11.7.11.7.1
DIAMONDN/AN/A0.9.220.9.22N/A
FastQC0.11.20.11.20.11.20.11.20.11.2
JRE (java)1.8.01.8.0N/AN/AN/A
HMMER3.1b23.1b23.1b23.1b23.1b2
KrakenN/AN/A1.01.0N/A
MACS1.4.21.4.21.4.21.4.2N/A
MAFFT7.2127.2127.2127.2127.212

MetaPhlAn2

2.0.0N/AN/A2.0.02.0.02.0.0N/A
MrBayes3.2.33.2.33.2.33.2.33.2.3
peak2gene1.021.021.021.02N/A
perl5.10.0.5 (32-bit)24.35.1024.0.5N/AN/AN/A
PhyML2012041220120412201204122012041220120412
python2.7.52.7.52.7.52.7.52.7.5
RscriptR is not included into the External Tools Packages. However, it may be installed using the UGENE Online Installer package.
samtools0.1.190.1.190.1.190.1.190.1.19
SeqPos1.011.011.011.01N/A
SnpEff4.3i4.3i4.3i4.3i4.3i
SPAdesN/AN/A3.12.03.12.0N/A
SpideyVersion not specifiedVersion not specifiedN/AVersion not specifiedVersion not specified
StringTieN/AN/A1.3.4d1.3.4dN/A
T-Coffee8.998.9911.0011.0011.00
TopHatN/AN/A2.01.912.01.8b1N/A
Trimmomatic0.380.380.380.380.38
vcftools0.1.12b0.1.12b0.1.12b0.1.12b0.1.12b
WEVOTEN/AN/AVersion not specifiedVersion not specifiedN/A