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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 |