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- Download the tools executables, see links on the web page http://ugene.net/download-all.html:
- External Tools Package: the package contains all external tools except JRE (i.e. "java") and RScript.
- Java Runtime Environment (JRE): although UGENE is not a Java application, a few tools (e.g. FastQC, Trimmomatic) require JRE. Make sure JRE 8 or higher is installed.
RScript: R is currently used in UGENE for ChIP-Seq data analysis only.
- Configure the tools in UGENE: open the UGENE Application Settings dialog, select the "External Tools" page, and specify the external tools executables.
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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 into in the corresponding External Tools Package in the table below.
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| 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 |
| Bowtie2 | 2.4.2 | 2.4.2 | 2.4.2 |
| BWA | 0.7.17 | 0.7.17 | 0.7.17 |
| CAP3 | 1012/1521/07 | 1012/1521/07 | 10/15/07 |
| CEAS | 0.9.9.7 | 0.9.9.7 | 0.9.9.7 |
CLARK | 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 tools | 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 |
| JRE (java) | 1.8.0 | N/A | N/A |
| HMMER | 3.3.1 | 3.3.1 | 3.3.1 |
| Kraken | N/A | 1.0 | 1.0 |
| MACS | 1.4.2 | 1.4.2 | 1.4.2 |
| MAFFT | 7.475 | 7.475 | 7.475 |
MetaPhlAn2 | N/A | 2.0.0 | 2.0.0 |
| MrBayes | 3.2.3 | 3.2.3 | 3.2.3 |
| peak2gene | 1.02 | 1.02 | 1.02 |
| perl | 5.24.3 | N/A | 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. However, it may be installed using the UGENE Online Installer package. | ||
| samtools | 0.1.19 | 0.1.19 | 0.1.19 |
| SeqPos | 1.01 | 1.01 | 1.01 |
| 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 | 8.99 | 11.00 | 1113.0044 |
| TopHat | N/A | 2.1.1 | 2.1.1 |
| Trimmomatic | 0.39 | 0.39 | 0.39 |
| vcftools | 0.1.12b | 0.1.12b | 0.1.12b |
| WEVOTE | N/A | Version not specified | Version not specified |