Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help
UGENE(1)		    General Commands Manual		      UGENE(1)

       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  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

       *      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.

       -ui    run GUI version of UGENE

       --help print  a	usage message briefly summarizing all command-line op-
	      tions 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
	      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			      UGENE(1)


Want to link to this manual page? Use this URL:

home | help