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External tool | Windows (64-bit) | macOS (64-bit) | Linux (64-bit) | |
---|---|---|---|---|
bigwig | 4 | 4 | 4 | |
bedtools | 2.29.2 | 2.31.0 | 2.31.0 | |
BLAST | 2.14.0 | 2.12.0 | 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 | 2.2.1 | 2.2.1 | |
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_192 | 11.0.11 | |
Kalign | 3.3.5 | 3.3.5 | 3.3.5 | |
Kraken (until UGENE v.40) | N/A | 1.0 | 1.0 | |
MAFFT | 7.520 | 7.520 | 7.520 | |
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 | 5.24.3 | N/A | N/A | |
PhyML Maximum 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 | 0.2.6 | |
vcfutils | Version not specified | Version not specified | Version not specified | |
SnpEff | 4.3i | 4.3i | 4.3i | |
SPAdes | N/A | 3.15.5 | 3.15.5 | |
Spidey | 1.0 | N/A | 1.0 | |
StringTie | N/A | 1.3.4d | 1.3.6 | |
TopHat | N/A | 2.1.1 | 2.1.1 | |
Trimmomatic | 0.39 | 0.39 | 0.39 | |
vcf-consensus | 0.1.16 | 0.1.16 | 0.1.16 | |
WEVOTE (until UGENE v.40) | N/A | 1.0 | 1.0 |
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