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| External tool | Windows (64-bit) | Windows (32-bit) | macOS (64-bit) | Linux (64-bit)Linux (32-bit) | |
|---|---|---|---|---|---|
| bedGraphToBigWig | 4 | N/A4 | 4 | N/A||
| bedtools | 2.20.1 | 2.20.12.20.1 | 2.20.1 | 2.20.1 | |
| BLAST+ | 2.2.30 | 2.2.302.2.30 | 2.2.30 | 2.2.30 | |
| Bowtie | 0.12.70.12.71.0.0 | 1.0.0 | 1.0.0 | ||
| Bowtie2 | 2.3.4.32.1.0 | 2.3.4.3 | 2.3.4.32.1.0 | ||
| BWA | 0.7.12 | 0.7.120.7.12 | 0.7.12 | 0.7.12 | |
| CAP3 | 12/21/07 | 12/21/0712/21/07 | 12/21/07 | 12/21/07 | |
| CEAS | 1.0.21.0.2 | 1.0.2 | 1.0.2 | N/A||
CLARK | N/AN/A | 1.2.4 (UGENE-customized) | 1.2.4 (UGENE-customized) | N/A||
| ClustalO | 1.2.1 | 1.2.11.2.1 | 1.2.1 | 1.2.1 | |
| ClustalW | 2.1 | 2.12.1 | 2.1 | 2.1 | |
| ConductGO | Version not specifiedVersion not specified | Version not specified | Version not specified | N/A||
| conservation_plot | 0.1.00.1.0 | 0.1.0 | 0.1.0 | N/A||
| Cufflinks tools | N/AN/A | 2.0.2 | 2.0.2 | N/A||
| Cutadapt | 1.7.1 | 1.7.11.7.1 | 1.7.1 | 1.7.1 | |
| DIAMOND | N/AN/A | 0.9.22 | 0.9.22 | N/A||
| FastQC | 0.11.2 | 0.11.20.11.2 | 0.11.2 | 0.11.2 | |
| JRE (java) | 1.8.01.8.0 | N/AN/A | N/A | ||
| HMMER | 3.1b2 | 3.1b23.1b2 | 3.1b2 | 3.1b2 | |
| Kraken | N/AN/A | 1.0 | 1.0 | N/A||
| MACS | 1.4.21.4.2 | 1.4.2 | 1.4.2 | N/A||
| MAFFT | 7.212 | 7.2127.212 | 7.212 | 7.212 | |
MetaPhlAn2 | N/AN/A | 2.0.0 | 2.0.0 | N/A||
| MrBayes | 3.2.3 | 3.2.33.2.3 | 3.2.3 | 3.2.3 | |
| peak2gene | 1.021.02 | 1.02 | 1.02 | N/A||
| perl | 5.24.3 | 5.24.0 | N/AN/A | N/A | |
| PhyML | 20120412 | 2012041220120412 | 20120412 | 20120412 | |
| python | 2.7.5 | 2.7.52.7.5 | 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 | 0.1.190.1.19 | 0.1.19 | 0.1.19 | |
| SeqPos | 1.011.01 | 1.01 | 1.01 | N/A||
| SnpEff | 4.3i | 4.3i4.3i | 4.3i | 4.3i | |
| SPAdes | N/AN/A | 3.12.0 | 3.12.0 | N/A||
| Spidey | Version not specifiedVersion not specified | N/A | Version not specifiedVersion not specified | ||
| StringTie | N/AN/A | 1.3.4d | 1.3.4d | N/A||
| T-Coffee | 8.998.9911.00 | 11.00 | 11.00 | ||
| TopHat | N/AN/A | 2.1.1 | 2.1.1 | N/A||
| Trimmomatic | 0.38 | 0.380.38 | 0.38 | 0.38 | |
| vcftools | 0.1.12b | 0.1.12b0.1.12b | 0.1.12b | 0.1.12b | |
| WEVOTE | N/AN/A | Version not specified | Version not specified | N/A||