.TH UGENE 1 "11 February 2011"
.SH NAME
\fBUGENE\fP \- integrated bioinformatics suite

.SH SYNOPSIS
.B ugene
.RI -ui
.P
.B ugene 
.RI [ OPTIONS ]

.SH DESCRIPTION
\fBUGENE\fP is a cross-platform environment for DNA and protein
sequence analysis. \fBUGENE\fP 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 \fBUGENE\fP:
.IP *
View and analysis of annotated DNA or protein sequences
.IP *
Chromatograms visualization and editing
.IP *
Integrated 3D viewer for files in PDB and MMDB formats
.IP *
Integrated support of search requests to NCBI databases
.IP *
Multiple sequence alignment using MUSCLE3, MUSCLE4 and KAlign
.IP *
HMM profiles build and search, based on the source of HMMER2 and HMMER3
.IP *
Modern protein secondary structure prediction algorithms based on GORIV and PsiPred
.IP *
Phylogenetic analysis with Phylip
.IP *
PCR Primers design using Primer3 package
.IP *
Cloning in silico
.IP *
Search for transcription factor binding sites in DNA sequences using SITECON
.IP *
Search for restriction enzymes and integration with REBASE
.IP *
Search for direct and invert repeats
.IP *
DNA reference assembly using Bowtie
.IP *
Protein back translation
.IP *
Search for ORFs
.IP *
Designer for complex computational workflows and queries

.PP
\fBUGENE\fP has modular structure and almost all its functionality comes
within plugins. Internally \fBUGENE\fP is designed with support of parallelism
to make profit from using multicore computers. Every computational task
in \fBUGENE\fP is performed in background and does not block user interaction
with graphical interface.

.SH OPTIONS
.TP
.B -ui
run GUI version of \fBUGENE\fP
.TP
.B --help
print a usage message briefly summarizing all command-line options and the program version, then exit.
.TP
.B --license
dump license information
.TP
.B --task=<path-to-schema or schema-name> [schema-options]
run given workflow schema
.TP
.B --status-bar-hide
don't show task status bar
.TP
.B --ini-file=<path-to-settings-file>
load custom UGENE settings file
.TP
.B --log-no-show-level
don't show message level at log
.TP
.B --log-no-show-date
don't show date&time info at log
.TP
.B --log-no-show-category
don't show message category at log
.TP
.B --log-level-trace
show trace log messages
.TP
.B --log-level-none
don't show log messages
.TP
.B --log-level-info
show error and info log messages (default)
.TP
.B --log-level-error
show only error log messages
.TP
.B --log-level-details
show details log messages
.TP
.B --log-color-output
colored output messages
.TP
.B --task-remote-machine=<path-to-machine-file>
run provided tasks on given remote machine
.TP
.B --ugene-stay-alive
do not stop ugene after finishing given tasks
.TP
.B --transl=<language-code>
load translations of specified language. Language is specified as a two-letter ISO 639 language code

.SH COMMANDS
.TP
\fBUGENE\fP has commands for most significant features. Commands can be run as
.RS 
\fBugene\fP <command-name> [command-arguments]
.RE
.RS
\fBugene\fP --task=<command-name> [command-arguments]
.RE
See help for each command running \fBugene\fP --help=<command-name>.
.RE
List of available commands can be dumped using \fBugene\fP --help.
.SH BUGS
If you find a bug, please report it at ugene@unipro.ru.

.SH AUTHOR
\fBugene\fP was created by Unipro (http://unipro.ru)