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UGENE provides GUI for a lot of different bioinformatics tools. A tool is supplied either as embedded or external:

  • 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 tool as a workflow element in the Workflow Designer. See "Custom External Tools" documentation chapter for details.

Specify integrated external tools in the installed package

Most of the external tools (if available on the target operating system) are installed by default in the Online Installer.

One can specify the tools manually:

  1.  Download the tools executables, see links on the web page http://ugene.net/download-all.html:
    • External Tools Package: the package contains all external tools except JRE (i.e. "java") and RScript.
    • Java Runtime Environment (JRE): although UGENE is not a Java application, a few tools (e.g. FastQC, Trimmomatic) require JRE. Make sure JRE 8 or higher is installed.
    • RScript: R is currently used in UGENE for ChIP-Seq data analysis only.

  2. Configure the tools in UGENE: open the UGENE Application Settings dialog, select the "External Tools" page, and specify the external tools executables.

Integrated external tools

See the list of the currently integrated external tools, information about their availability on different operating systems, and the version included in the corresponding External Tools Package in the table below.


External toolWindows (64-bit)macOS (64-bit)Linux (64-bit)
bigwig444
bedtools2.29.22.29.22.29.2
BLAST+2.10.1+2.10.1+2.10.1+
Bowtie1.3.01.3.01.3.0
Bowtie22.4.22.4.22.4.2
BWA

0.7.17-r1188

0.7.17-r11880.7.17-r1188
CAP312/21/07

12/21/07

10/15/07
CistromeCEAS Tools (need Rscript)0.9.9.70.9.9.70.9.9.7

conservation_plot (need Rscript)

0.10.10.1

go_analysis (need Rscript)

1.0.11.0.11.0.1
MACS1.4.21.4.21.4.2

peak2gene

1.021.021.02

seqpos (need Rscript)

2.02.02.0

CLARK

N/A1.2.4 (UGENE-customized)1.2.4 (UGENE-customized)
ClustalO1.2.21.2.31.2.4
ClustalW2.12.12.1
CufflinksN/A2.0.22.0.2
cutadapt1.7.11.7.11.7.1
DIAMONDN/A0.9.220.9.22
FastQC0.11.90.11.90.11.9
HMMER3.3.13.3.13.3.1
JRE (java)

1.8.0_192

1.8.0_1921.8.0_192
KrakenN/A1.01.0
MAFFT7.4757.4757.475

MetaPhlAn2

N/A2.7.72.0.0
MrBayes3.2.33.2.33.2.3
Perl5.24.35.18.2N/A
PhyML201204122012041220120412
pythonpython2.7.52.7.52.7.5
BioN/A1.731.73
django1, 5, 11, 5, 11, 5, 1
numpy1.7.11.16.01.16.0
RscriptR is not included into the External Tools Packages.
SAMtoolsBCFtools0.1.190.1.190.1.19
SAMtools0.1.190.1.190.1.19
Tabix0.2.50.2.60.2.5
vcfutilsVersion not specifiedVersion not specifiedVersion not specified
SnpEff4.3i4.3i4.3i
SPAdesN/A3.14.13.14.1
SpideyVersion not specifiedN/AVersion not specified
StringTieN/A1.3.4d1.3.4d
T-Coffee8.9911.0013.44
TopHatN/A2.1.12.1.1
Trimmomatic0.390.390.39
vcf-consensus0.1.12b0.1.12b0.1.12b
WEVOTEN/A1.01.0



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