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UGENE(1)		    General Commands Manual		      UGENE(1)

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  computa-
       tional  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  parallel-
       ism  to make profit from	using multicore	computers. Every computational
       task in UGENE is	performed in background	and does not block user	inter-
       action with graphical interface.

OPTIONS
       -ui    run GUI version of UGENE

       --help print  a	usage message briefly summarizing all command-line op-
	      tions 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)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | COMMANDS | BUGS | AUTHOR

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