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- 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.
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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) | |||||
|---|---|---|---|---|---|---|---|---|
| bigwig | 4 | 4 | 4 | |||||
| bedtools | 2.29.2 | 2.29.2 | 2.29.2 | |||||
| BLAST | +2.1014.10 | 2.1014.10 | 2.1014.10 | |||||
| Bowtie | 1.3.0 | 1.3.0 | 1.3.0 | |||||
| Bowtie2 | 2.4.2 | 2.4.2 | 2.4.2 | |||||
| BWA | 0.7.17-r1188 | 0.7.17-r1188 | 0.7.17-r1188 | |||||
| CAP3 | 12/21/07 | 12/21/07 | 10/15/07 | |||||
| Cistrome (until UGENE v.41) | CEAS Tools (need Rscript) | 0.9.9.7 | 0.9.9.7 | 0.9.9.7 | ||||
conservation_plot (need Rscript) | 0.1 | 0.1 | 0.1 | |||||
go_analysis (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 (until UGENE v.40) | N/A | 1.2.4 (UGENE-customized) | 1.2.4 (UGENE-customized) | |||||
| ClustalO | 1.2.2 | 1.2.3 | 1.2.4 | |||||
| ClustalW | 2.1 | 2.1 | 2.1 | |||||
| ConductGO | Version not specified | Version not specified | Version not specified | |||||
| conservation_plot | 0.1.0 | 0.1.0 | 0.1.0 | |||||
| Cufflinks | N/A | 2.0.2 | 2.0.2 | |||||
| DIAMOND (until UGENE v.40) | N/A | 20.09.2222 | 0.09.222 | |||||
| FastQC | 0.12.1 | 0.712.1 | 0.12.1 | |||||
| FastTree | 2. | 71. | 111 | 2.1. | 711 | 2.1.11 | ||
| DIAMOND | N/A | 2.0.8 | 0.9.22 | |||||
| FastQC | 0.11.9 | 0.11.9 | 0.11.9HMMER | 3.3.1 | 3.3.1 | 3.3.1 | ||
IQ-TREE | 1.6.12 | 1.6.12 | 1.6.12 | |||||
| JRE (java) | 1.8.0_192 | 1.8.0_281192 | 1.8.0_192 | |||||
Kalign | 3.35.15 | 3.35.15 | 3.35.1 | Kraken5 | ||||
| Kraken (until UGENE v.40) | N/A | 1.1.10 | 1.0 | |||||
| MAFFT | 17.4.25201 | 7.4.25201 | 7.4.2520 | MAFFT|||||
| mfold | 73. | 4756 | 73. | 4756 | 73. | 475MetaPhlAn26 | ||
MetaPhlAn2 (until UGENE v.40) | N/A | 2.7.7 | 2.0.0 | |||||
| MrBayes | 3.2.3 | 3.2.3 | 3.2.3 | |||||
| peak2gene | 1.02 | 1.02 | 1.02 | |||||
| Perl | 5.24.3 | 5.18.2 | N/A | |||||
| PhyML Maximum Likelihood | 3.3.20220408 | 20120412 | 2012041220120412 | |||||
| Python3 | python | 2.7.5 | 2.7.5 | 2.7.53.12.1 | 3.12.1 | 3.12.1 | ||
| cutadupt | 4.6 | 4.6 | 4.6 | |||||
| Rscript | R is not included into the External Tools Packages. | However, it may be installed using the UGENE Online Installer package.samtools|||||||
| SAMtools | BCFtools | 0.1.19 | 0.1.19 | 0.1.19 | ||||
| SAMtools | 0.1.0119 | 0.1.0119 | 0.1.01.19 | |||||
| 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 | 21.13.54d | 1.3.4d | T-Coffee | 8.99 | 11.00 | 13.44 | |
| TopHat | N/A | 2.1.1 | 2.1.1 | |||||
| Trimmomatic | 0.39 | 0.39 | 0.39 | vcftools|||||
| vcf-consensus | 0.1.12b | 0.1.12b | 0.1.12b | |||||
| WEVOTE (until UGENE v.40) | N/A | Version not specified | Version not specified1.0 | 1.0 | ||||