NAME

       UGENE - 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:

       *      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.

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)

                                         11 February 2011                                UGENE(1)