UGENE provides GUI for a lot of different bioinformatics tools. A tool is supplied either as embedded or external:
- 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: 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.
Specify external tools in the installed package
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:
...
| 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 | 2.2.26 | 2.2.26 | 2.2.26 | 2.2.26 | 2.2.26 | |||||||||
| 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 | 2.1.0 | 2.0.6 | 2.1.0 | 2.1.0 | 2.1.0 | |||||||||
| BWA | 0.7.12 | 0.7.12 | 0.7.12 | 0.7.12 | 0.7.12 | |||||||||
| CAP3 | 12/21/07 | CEAS | TODO | 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 | TODO | Version not specified | Version not specified | Version not specified | Version not specified | N/A | ||||||||
| conservation_plot | TODO | 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) | JRE is not included into the External Tools Packages. | |||||||||||||
| 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 | 7.212 | 7.212 | 7.212 | 7.212 | 7.212 | |||||||||
| 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 | 5.10.0.5 (32-bit) | 5.10.0.5 | 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 | SeqPos | TODO | 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 | 2.0.9 | 2.0.8b | 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 | |||||||||