ugene man page

UGENE ā€” integrated bioinformatics suite

Synopsis

ugene -ui

ugene [Options]

Description

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:

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.

Options

-ui

run GUI version of UGENE

--help

print a usage message briefly summarizing all command-line options and the program version, then exit.

--license

dump license information

--task=<path-to-schema or schema-name> [schema-options]

run given workflow schema

--status-bar-hide

don't show task status bar

--ini-file=<path-to-settings-file>

load custom UGENE settings file

--log-no-show-level

don't show message level at log

--log-no-show-date

don't show date&time info at log

--log-no-show-category

don't show message category at log

--log-level-trace

show trace log messages

--log-level-none

don't show log messages

--log-level-info

show error and info log messages (default)

--log-level-error

show only error log messages

--log-level-details

show details log messages

--log-color-output

colored output messages

--task-remote-machine=<path-to-machine-file>

run provided tasks on given remote machine

--ugene-stay-alive

do not stop ugene after finishing given tasks

--transl=<language-code>

load translations of specified language. Language is specified as a two-letter ISO 639 language code

Commands

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.

Bugs

If you find a bug, please report it at ugene@unipro.ru.

Author

ugene was created by Unipro (http://unipro.ru)

Info

11 February 2011