UGENE provides GUI for a lot of different bioinformatics tools. A tool is supplied either as embedded or external:
The external tools (if available on the target operating system) are provided by default in the Online Installer, Full and NGS UGENE packages.
One can specify the tools manually:
RScript: R is currently used in UGENE for ChIP-Seq data analysis only.
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 tool | Windows (64-bit) | Windows (32-bit) | macOS (64-bit) | Linux (64-bit) | Linux (32-bit) |
---|---|---|---|---|---|
bedGraphToBigWig | 4 | N/A | 4 | 4 | N/A |
bedtools | 2.20.1 | 2.20.1 | 2.20.1 | 2.20.1 | 2.20.1 |
BLAST+ | 2.2.30 | 2.2.30 | 2.2.30 | 2.2.30 | 2.2.30 |
Bowtie | 0.12.7 | 0.12.7 | 1.0.0 | 1.0.0 | 1.0.0 |
Bowtie2 | 2.3.4.3 | 2.1.0 | 2.3.4.3 | 2.3.4.3 | 2.1.0 |
BWA | 0.7.12 | 0.7.12 | 0.7.12 | 0.7.12 | 0.7.12 |
CAP3 | 12/21/07 | 12/21/07 | 12/21/07 | 12/21/07 | 12/21/07 |
CEAS | 1.0.2 | 1.0.2 | 1.0.2 | 1.0.2 | N/A |
CLARK | N/A | N/A | 1.2.4 (UGENE-customized) | 1.2.4 (UGENE-customized) | N/A |
ClustalO | 1.2.1 | 1.2.1 | 1.2.1 | 1.2.1 | 1.2.1 |
ClustalW | 2.1 | 2.1 | 2.1 | 2.1 | 2.1 |
ConductGO | Version not specified | Version not specified | Version not specified | Version not specified | N/A |
conservation_plot | 0.1.0 | 0.1.0 | 0.1.0 | 0.1.0 | N/A |
Cufflinks tools | N/A | N/A | 2.0.2 | 2.0.2 | N/A |
Cutadapt | 1.7.1 | 1.7.1 | 1.7.1 | 1.7.1 | 1.7.1 |
DIAMOND | N/A | N/A | 0.9.22 | 0.9.22 | N/A |
FastQC | 0.11.2 | 0.11.2 | 0.11.2 | 0.11.2 | 0.11.2 |
JRE (java) | 1.8.0 | 1.8.0 | N/A | N/A | N/A |
HMMER | 3.1b2 | 3.1b2 | 3.1b2 | 3.1b2 | 3.1b2 |
Kraken | N/A | N/A | 1.0 | 1.0 | N/A |
MACS | 1.4.2 | 1.4.2 | 1.4.2 | 1.4.2 | N/A |
MAFFT | 7.450 | 7.212 | 7.450 | 7.450 | 7.212 |
MetaPhlAn2 | N/A | N/A | 2.0.0 | 2.0.0 | N/A |
MrBayes | 3.2.3 | 3.2.3 | 3.2.3 | 3.2.3 | 3.2.3 |
peak2gene | 1.02 | 1.02 | 1.02 | 1.02 | N/A |
perl | 5.24.3 | 5.24.0 | N/A | N/A | N/A |
PhyML | 20120412 | 20120412 | 20120412 | 20120412 | 20120412 |
python | 2.7.5 | 2.7.5 | 2.7.5 | 2.7.5 | 2.7.5 |
Rscript | R is not included into the External Tools Packages. However, it may be installed using the UGENE Online Installer package. | ||||
samtools | 0.1.19 | 0.1.19 | 0.1.19 | 0.1.19 | 0.1.19 |
SeqPos | 1.01 | 1.01 | 1.01 | 1.01 | N/A |
SnpEff | 4.3i | 4.3i | 4.3i | 4.3i | 4.3i |
SPAdes | N/A | N/A | 3.12.0 | 3.12.0 | N/A |
Spidey | Version not specified | Version not specified | N/A | Version not specified | Version not specified |
StringTie | N/A | N/A | 1.3.4d | 1.3.4d | N/A |
T-Coffee | 8.99 | 8.99 | 11.00 | 11.00 | 11.00 |
TopHat | N/A | N/A | 2.1.1 | 2.1.1 | N/A |
Trimmomatic | 0.38 | 0.38 | 0.38 | 0.38 | 0.38 |
vcftools | 0.1.12b | 0.1.12b | 0.1.12b | 0.1.12b | 0.1.12b |
WEVOTE | N/A | N/A | Version not specified | Version not specified | N/A |