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| 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 | 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) | 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 | 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 | ||