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| External tool | Windows (64-bit) | macOS (64-bit) | Linux (64-bit) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bedGraphToBigWigbigwig | 4 | 4 | 4 | ||||||||||
| Bedtoolsbedtools | 2.29.2 | 2.2931.20 | 2.2931.20 | ||||||||||
| BLAST+ | 2.1014.1+0 | 2 2.1012.1+0 | 2.1014.1+0 | ||||||||||
| Bowtie | 1.3.0 | 1.3.0 | 1.3.0 | ||||||||||
| Bowtie 2Bowtie2 | 2.4.2 | 2.4.2 | 2.4.2 | ||||||||||
| Burrows-Wheeler Aligner (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 | |||||||||
ConservationPlot conservation_plot (need Rscript) | 0.1 | 0.1 | 0.1 | ||||||||||
Conduct GO 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 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) | ||||||||||
| Clustal OmegaClustalO | 1.2.2 | 1.2.3 | 1.2.4 | ||||||||||
| ClustalW | 2.1 | 2.1 | 2.1 | ||||||||||
| Cufflinks | N/A | 2.02.21 | 2.02.21 | ||||||||||
| cutadapt (until UGENE v.49) | 1.7.1 | 1.7.1 | 1.7.1 | ||||||||||
| DIAMONDDIAMOND (until UGENE v.40) | N/A | 0.9.22 | 0.9.22 | ||||||||||
| FastQC | 0.1112.91 | 0.1112.91 | 0.12.1 | ||||||||||
| FastTree (since UGENE v.46) | 2.1.11 | .92.1.11 | 2.1.11 | ||||||||||
| HMMER | 3.3.1 | 3.3.1 | 3.3.1 | ||||||||||
IQ-TREE (since UGENE v.41) | 1.6.12 | 1.6.12 | 1.6.12 | ||||||||||
| JRE (java) | 1.8.0_192 | 1.8.0_192 | 1.8.0_192 | Kraken11.0.11 | |||||||||
Kalign | 3.3.5 | 3.3.5 | 3.3.5 | ||||||||||
| Kraken (until UGENE v.40) | N/A | 1.0 | 1.0 | ||||||||||
| MAFFT | 7.475520 | 7.475520 | 7.475 | MetaPhlAn2520 | |||||||||
| 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 | 20120412 | 20120412 | 20120412 | Python | 2.7.5 | 2.7.5 | 2.7.5Maximum Likelihood | 3.3.20220408 | 3.3.20220408 | 3.3.20220408 | |||
| Python3 | python | 3.12.1 | N/A | 3.12.1 | |||||||||
| Cutadapt | 4.6 | 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 | 1.3.4d | T-Coffee | Version not specified | 11.00 | 13.446 | ||||||
| TopHat | N/A | 2.1.1 | 2.1.1 | ||||||||||
| Trimmomatic | Version not specified | Version not specified0.39 | 0.39 | 0.39 | |||||||||
| vcf-consensus | Version not specified | Version not specified0.1.16 | 0.1.16 | 0.1.12b | WEVOTE16 | ||||||||
| WEVOTE (until UGENE v.40) | N/A | Version not specified | Version not specified1.0 | 1.0 | |||||||||