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| External tool | Windows (64-bit) | macOS (64-bit) | Linux (64-bit) | ||||||
|---|---|---|---|---|---|---|---|---|---|
| bigwig | 4 | 4 | 4 | ||||||
| bedtools | 2.29.2 | 2.29.2 | 2.29.2 | ||||||
| BLAST+ | 2.1014.1+0 | 2.1014.1+0 | 2.1014.1+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 | 2.0.2 | 2.0.2 | ||||||
| cutadapt | 1.7.1 | 1.7.1 | 1.7.1 | ||||||
| DIAMOND | DIAMOND (until UGENE v.40) | N/A | 0.9.22 | 0.9.22 | |||||
| FastQC | 0.1112.91 | 0.1112.91 | 0.12.1 | ||||||
| FastTree | 2.1.11 | .92.1.11 | 2.1.11 | ||||||
| HMMER | 3.3.1 | 3.3.1 | 3.3.1 | ||||||
IQ-TREE | 1.6.12 | 1.6.12 | 1.6.12 | ||||||
| JRE (java) | 1.8.0_192 | 1.8.0_192 | 1.8.0_192 | Kraken||||||
Kalign | 3.5.5 | 3.5.5 | 3.5.5 | ||||||
| Kraken (until UGENE v.40) | N/A | 1.0 | 1.0 | ||||||
| MAFFT | 7.475520 | 7.475520 | 7.475 | MetaPhlAn2.520 | |||||
| mfold | 3.6 | 3.6 | 3.6 | ||||||
MetaPhlAn2 (until UGENE v.40) | N/A | 2.7.7 | 2.0.0 | ||||||
| MrBayes | 3.2.3 | 3.2.3 | 3.2.3 | ||||||
| Perl | 5.24.3 | 5.18.2 | N/A | ||||||
| PhyML | 20120412Maximum Likelihood | 3.3.20220408 | 20120412 | 20120412 | |||||
| Python3 | python | 23.712.512 | 3.712.512 | 3.7.5 | |||||
| Bio | N/A | 1.73 | 1.73 | ||||||
| django | 1, 5, 1 | 1, 5, 1 | 1, 5, 1 | ||||||
| numpy | 1.7.1 | 1.16.0 | 1.16.012.1 | ||||||
| cutadupt | 4.6 | 4.6 | 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 | 0.2.5 | ||||||
| vcfutils | Version not specified | Version not specified | Version not specified | ||||||
| SnpEff | 4.3i | 4.3i | 4.3i | ||||||
| SPAdes | N/A | 3.14.1 | 3.14.1 | ||||||
| Spidey | Version not specified | N/A | Version not specified | ||||||
| StringTie | N/A | 1.3.4d | 1.3.4d | T-Coffee | 8.99 | 11.00 | 13.44 | ||
| TopHat | N/A | 2.1.1 | 2.1.1 | ||||||
| Trimmomatic | 0.39 | 0.39 | 0.39 | ||||||
| vcf-consensus | 0.1.12b | 0.1.12b | 0.1.12b | ||||||
| WEVOTEWEVOTE (until UGENE v.40) | N/A | 1.0 | 1.0 | ||||||