UGENE provides GUI for a lot of different bioinformatics tools. A tool is supplied either as embedded or external:
The external tools (if available on the target operating system) are provided by default in the Online Installer, Full and NGS UGENE packages.
One can specify the tools manually:
RScript: R is currently used in UGENE for ChIP-Seq data analysis only.
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 |