ugene man page

UGENE — integrated bioinformatics suite


ugene -ui

ugene [Options]


UGENE is a cross-platform environment for DNA and protein sequence analysis. UGENE integrates the most popular bioinformatics computational algorithms and provides both GUI and command line interface for performing complex analysis of the genomic data.

The main features of UGENE:

View and analysis of annotated DNA or protein sequences
Chromatograms visualization and editing
Integrated 3D viewer for files in PDB and MMDB formats
Integrated support of search requests to NCBI databases
Multiple sequence alignment using MUSCLE3, MUSCLE4 and KAlign
HMM profiles build and search, based on the source of HMMER2 and HMMER3
Modern protein secondary structure prediction algorithms based on GORIV and PsiPred
Phylogenetic analysis with Phylip
PCR Primers design using Primer3 package
Cloning in silico
Search for transcription factor binding sites in DNA sequences using SITECON
Search for restriction enzymes and integration with REBASE
Search for direct and invert repeats
DNA reference assembly using Bowtie
Protein back translation
Search for ORFs
Designer for complex computational workflows and queries

UGENE has modular structure and almost all its functionality comes within plugins. Internally UGENE is designed with support of parallelism to make profit from using multicore computers. Every computational task in UGENE is performed in background and does not block user interaction with graphical interface.


run GUI version of UGENE
print a usage message briefly summarizing all command-line options and the program version, then exit.
dump license information
--task=<path-to-schema or schema-name> [schema-options]
run given workflow schema
don't show task status bar
load custom UGENE settings file
don't show message level at log
don't show date&time info at log
don't show message category at log
show trace log messages
don't show log messages
show error and info log messages (default)
show only error log messages
show details log messages
colored output messages
run provided tasks on given remote machine
do not stop ugene after finishing given tasks
load translations of specified language. Language is specified as a two-letter ISO 639 language code


UGENE has commands for most significant features. Commands can be run as

ugene <command-name> [command-arguments]

ugene --task=<command-name> [command-arguments]

See help for each command running ugene --help=<command-name>. List of available commands can be dumped using ugene --help.


If you find a bug, please report it at


ugene was created by Unipro (


11 February 2011