Unipro UGENE Online User Manual v. 1.31
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  1.  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.

  2. 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 toolWindows 64-bitmacOS 64-bitLinux 64-bitWindows 32-bitLinux 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