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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+ | 2.1014.1+0 | 2 2.1012.1+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 | 2.02.21 | 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 | 0.1112.91 | ||||||
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 | 7.475520 | 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 | pythonMaximum Likelihood | 3.3.20220408 | 3.3.20220408 | 3.3.20220408 | ||
Python3 | python | 23.7.5 | 2.7.5 | 2.7.5 | Bio12.1 | N/A | 3.12.1 | ||
Cutadapt | 4.6 | N/A | 1.73 | 1.734.6 | |||||
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 |