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External tool | Windows (64-bit) | macOS (64-bit) | Linux (64-bit) | ||||||
---|---|---|---|---|---|---|---|---|---|
bedGraphToBigWigbigwig | 4 | 4 | 4 | ||||||
Bedtoolsbedtools | 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 | ||||||
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 | 2.0.2 | 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 Maximum Likelihood | 3.3.20220408 | 20120412 | 20120412 | 20120412 | Python | 2.7.5 | 2.7.5 | 2.7.||
Python3 | python | 3.12.1 | 3.12.1 | 3.12.1 | |||||
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 |