...
| External tool | Windows (64-bit) | macOS (64-bit) | Linux (64-bit) | |||
|---|---|---|---|---|---|---|
| bigwig | 4 | 4 | 4 | |||
| bedtools | 2.29.2 | 2.2931.20 | 2.2931.20 | |||
| BLAST | 2.14.0 | 2 2.1412.0 | 2.14.0 | |||
| Bowtie | 1.3.0 | 1.3.0 | 1.3.0 | |||
| Bowtie2 | 2.4.2 | 2.4.2 | 2.4.2 | |||
| BWA | 0.7.17-r1188 | 0.7.17-r1188 | 0.7.17-r1188 | |||
| CAP3 | 12/21/07 | 12/21/07 | 10/15/07 | |||
| Cistrome (until UGENE v.41) | CEAS Tools (need Rscript) | 0.9.9.7 | 0.9.9.7 | 0.9.9.7 | ||
conservation_plot (need Rscript) | 0.1 | 0.1 | 0.1 | |||
go_analysis (need Rscript) | 1.0.1 | 1.0.1 | 1.0.1 | |||
| MACS | 1.4.2 | 1.4.2 | 1.4.2 | |||
peak2gene | 1.02 | 1.02 | 1.02 | |||
seqpos (need Rscript) | 2.0 | 2.0 | 2.0 | |||
CLARK (until UGENE v.40) | 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 | |||
| Cufflinks | N/A | 2.2.01 | 2.2 | 2.0.2 | DIAMOND.1 | |
| cutadapt (until UGENE v.49) | 1.7.1 | 1.7.1 | 1.7.1 | |||
| DIAMOND (until UGENE v.40) | N/A | 0.9.22 | 0.9.22 | |||
| FastQC | 0.12.1 | 0.12.1 | 0.12.1 | |||
| FastTree (since UGENE v.46) | 2.1.11 | 2.1.11 | 2.1.11 | |||
| HMMER | 3.3.1 | 3.3.1 | 3.3.1 | |||
IQ-TREETREE (since UGENE v.41) | 1.6.12 | 1.6.12 | 1.6.12 | |||
| JRE (java) | 1.8.0_192 | 1.8.0_1921 | 11.80.0_19211 | |||
Kalign | 3.53.5 | 3.53.5 | 3.53.5 | |||
| KrakenKraken (until UGENE v.40) | N/A | 1.0 | 1.0 | |||
| MAFFT | 7.520 | 7.520 | 7.520 | |||
| mfold | 3.6 | 3.6 | 3.6 | |||
MetaPhlAn2 | MetaPhlAn2 (until UGENE v.40) | N/A | 2.7.7 | 2.0.0 | ||
mfold (since UGENE v.50) | 3.6 | 3.6 | 3.6 | |||
| MrBayes | 3.2.3 | 3.2.3 | 3.2.3 | |||
| Perl | 5.24.35.18.2 | N/A | N/A | |||
| PhyML Maximum Likelihood | 3.3.20220408 | 20120412 | 201204123.3.20220408 | 3.3.20220408 | ||
| Python3 | python | 3.12.13.12.1 | N/A | 3.12.1 | ||
| cutaduptCutadapt | 4.64.6 | N/A | 4.6 | |||
| Rscript | R is not included into the External Tools Packages. | |||||
| SAMtools | BCFtools | 0.1.19 | 0.1.19 | 0.1.19 | ||
| SAMtools | 0.1.19 | 0.1.19 | 0.1.19 | |||
| Tabix | 0.2.5 | 0.2.6 | 0.2.56 | |||
| vcfutils | Version not specified | Version not specified | Version not specified | |||
| SnpEff | 4.3i | 4.3i | 4.3i | |||
| SPAdes | N/A | 3.1415.15 | 3.1415.15 | |||
| Spidey | Version not specified1.0 | N/A | Version not specified1.0 | |||
| StringTie | N/A | 1.3.4d | 1.3.4d6 | |||
| TopHat | N/A | 2.1.1 | 2.1.1 | |||
| Trimmomatic | 0.39 | 0.39 | 0.39 | |||
| vcf-consensus | 0.1.12b16 | 0.1.12b16 | 0.1.12b | WEVOTE16 | ||
| WEVOTE (until UGENE v.40) | N/A | 1.0 | 1.0 | |||