UGENE provides GUI for a lot of different bioinformatics tools. A tool is supplied either as embedded or external:
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:
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 the version included in the corresponding External Tools Package in the table below.
External tool | Windows (64-bit) | macOS (64-bit) | Linux (64-bit) | |
---|---|---|---|---|
bedGraphToBigWig | 4 | 4 | 4 | |
Bedtools | 2.29.2 | 2.29.2 | 2.29.2 | |
BLAST+ | 2.10.1+ | 2.10.1+ | 2.10.1+ | |
Bowtie | 1.3.0 | 1.3.0 | 1.3.0 | |
Bowtie 2 | 2.4.2 | 2.4.2 | 2.4.2 | |
Burrows-Wheeler Aligner (BWA) | 0.7.17-r1188 | 0.7.17-r1188 | 0.7.17-r1188 | |
CAP3 | 12/21/07 | 12/21/07 | 10/15/07 | |
Cistrome | CEAS (need Rscript) | 0.9.9.7 | 0.9.9.7 | 0.9.9.7 |
ConservationPlot (need Rscript) | 0.1 | 0.1 | 0.1 | |
Conduct GO (need Rscript) | 1.0.1 | 1.0.1 | 1.0.1 | |
MACS | 1.4.2 | 1.4.2 | 1.4.2 | |
peak2gene | 1.02 | 1.02 | 1.02 | |
SeqPos (need Rscript) | 2.0 | 2.0 | 2.0 | |
CLARK | N/A | 1.2.4 (UGENE-customized) | 1.2.4 (UGENE-customized) | |
Clustal Omega | 1.2.2 | 1.2.3 | 1.2.4 | |
ClustalW | 2.1 | 2.1 | 2.1 | |
Cufflinks | N/A | 2.0.2 | 2.0.2 | |
cutadapt | 1.7.1 | 1.7.1 | 1.7.1 | |
DIAMOND | N/A | 0.9.22 | 0.9.22 | |
FastQC | 0.11.9 | 0.11.9 | 0.11.9 | |
HMMER | 3.3.1 | 3.3.1 | 3.3.1 | |
JRE (java) | 1.8.0_192 | 1.8.0_192 | 1.8.0_192 | |
Kraken | N/A | 1.0 | 1.0 | |
MAFFT | 7.475 | 7.475 | 7.475 | |
MetaPhlAn2 | N/A | 2.7.7 | 2.0.0 | |
MrBayes | 3.2.3 | 3.2.3 | 3.2.3 | |
Perl | 5.24.3 | 5.18.2 | N/A | |
PhyML | 20120412 | 20120412 | 20120412 | |
Python | 2.7.5 | 2.7.5 | 2.7.5 | |
Rscript | R is not included into the External Tools Packages. | |||
SAMtools | BCFtools | 0.1.19 | 0.1.19 | 0.1.19 |
SAMtools | 0.1.19 | 0.1.19 | 0.1.19 | |
Tabix | 0.2.5 | 0.2.6 | 0.2.5 | |
vcfutils | Version not specified | Version not specified | Version not specified | |
SnpEff | 4.3i | 4.3i | 4.3i | |
SPAdes | N/A | 3.14.1 | 3.14.1 | |
Spidey | Version not specified | N/A | Version not specified | |
StringTie | N/A | 1.3.4d | 1.3.4d | |
T-Coffee | Version not specified | 11.00 | 13.44 | |
TopHat | N/A | 2.1.1 | 2.1.1 | |
Trimmomatic | Version not specified | Version not specified | 0.39 | |
vcf-consensus | Version not specified | Version not specified | 0.1.12b | |
WEVOTE | N/A | Version not specified | Version not specified |