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

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:
  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 version included into the corresponding External Tools Package in the table below.


External toolWindows (64-bit)macOS (64-bit)Linux (64-bit)
bedGraphToBigWig444
bedtools2.20.12.20.12.20.1
BLAST+2.2.302.2.302.2.30
Bowtie0.12.71.0.01.0.0
Bowtie22.3.4.32.3.4.32.3.4.3
BWA0.7.120.7.120.7.12
CAP312/21/07

12/21/07

12/21/07
CEAS1.0.21.0.21.0.2

CLARK

N/A1.2.4 (UGENE-customized)1.2.4 (UGENE-customized)
ClustalO1.2.11.2.11.2.1
ClustalW2.12.12.1
ConductGOVersion not specifiedVersion not specifiedVersion not specified
conservation_plot0.1.00.1.00.1.0
Cufflinks toolsN/A2.0.22.0.2
Cutadapt1.7.11.7.11.7.1
DIAMONDN/A0.9.220.9.22
FastQC0.11.20.11.20.11.2
JRE (java)1.8.0N/AN/A
HMMER3.1b23.1b23.1b2
KrakenN/A1.01.0
MACS1.4.21.4.21.4.2
MAFFT7.4507.4507.450

MetaPhlAn2

N/A2.0.02.0.0
MrBayes3.2.33.2.33.2.3
peak2gene1.021.021.02
perl5.24.3N/AN/A
PhyML201204122012041220120412
python2.7.52.7.52.7.5
RscriptR is not included into the External Tools Packages. However, it may be installed using the UGENE Online Installer package.
samtools0.1.190.1.190.1.19
SeqPos1.011.011.01
SnpEff4.3i4.3i4.3i
SPAdesN/A3.12.03.12.0
SpideyVersion not specifiedN/AVersion not specified
StringTieN/A1.3.4d1.3.4d
T-Coffee8.9911.0011.00
TopHatN/A2.1.12.1.1
Trimmomatic0.380.380.38
vcftools0.1.12b0.1.12b0.1.12b
WEVOTEN/AVersion not specifiedVersion not specified