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- Download the tools executables, see links on the "Download UGENE and components" page:
- External Tool Package: the package contains all external tools except JRE (i.e. "java") and RScript.
- Java Runtime Environment (JRE): although UGENE is not a Java application, a few tools (e.g. FastQC, Trimmomatic) require JRE. Make sure JRE 8 or higher is installed.
RScript: R is currently used in UGENE for ChIP-Seq data analysis only.
- Configure the tools in UGENE: open the UGENE Application Settings dialog, select the "External Tools" page and specify the external tools executables.
Integrated external tools
The following external tools are currently integrated into UGENE:
External tool | Windows 64-bit | macOS 64-bit | Linux 64-bit | Windows 32-bit | Linux 32-bit |
---|---|---|---|---|---|
bedGraphToBigWig | |||||
bedtools | |||||
BLAST | |||||
BLAST+ | |||||
Bowtie | |||||
Bowtie2 | |||||
BWA | |||||
CAP3 | |||||
CEAS | |||||
CLARK | |||||
ClustalO | |||||
ClustalW | |||||
ConductGO | |||||
conservation_plot | |||||
Cufflinks tools | |||||
Cutadapt | |||||
DIAMOND | |||||
FastQC | |||||
HMMER | |||||
Kraken | |||||
MACS | |||||
MAFFT | |||||
MrBayes | |||||
PhyML | |||||
peak2gene | |||||
python | |||||
samtools | |||||
SeqPos | |||||
SnpEff | |||||
SPAdes | |||||
Spidey | |||||
StringTie | |||||
T-Coffee | |||||
TopHat | |||||
Trimmomatic | |||||
vcftools | |||||
WEVOTE |