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