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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 | MetaPhlAn2520 | |||
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 | 3.712.51 | 2.7.5 | |||
Bio | N/A | 1.73 | 1.73 | ||||
django | 1, 5, 1 | 1, 5, 1 | 1, 5, 1 | ||||
numpy | 1.7.1 | 1.16.0 | 1.16.03.12.1 | ||||
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||||
Version not specified | 11.00 | 13.44 | 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 specified0.1.12b | 0.1.12b | 0.1.12b | |||
WEVOTEWEVOTE (until UGENE v.40) | N/A | Version not specified | Version not specified1.0 | 1.0 |