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


External toolWindows (64-bit)macOS (64-bit)Linux (64-bit)
bedGraphToBigWig444
Bedtools2.29.22.29.22.29.2
BLAST+2.10.1+2.10.1+2.10.1+
Bowtie1.3.01.3.01.3.0
Bowtie 22.4.22.4.22.4.2
Burrows-Wheeler Aligner (BWA)

0.7.17-r1188

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

12/21/07

10/15/07
CistromeCEAS (need Rscript)0.9.9.70.9.9.70.9.9.7

ConservationPlot (need Rscript)

0.10.10.1

Conduct GO (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)
Clustal Omega1.2.21.2.31.2.4
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
Python2.7.52.7.52.7.5
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-CoffeeVersion not specified11.0013.44
TopHatN/A2.1.12.1.1
TrimmomaticVersion not specifiedVersion not specified0.39
vcf-consensusVersion not specifiedVersion not specified0.1.12b
WEVOTEN/AVersion not specifiedVersion not specified