1UGENE(1)                    General Commands Manual                   UGENE(1)
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NAME

6       UGENE - integrated bioinformatics suite
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SYNOPSIS

10       ugene -ui
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12       ugene [OPTIONS]
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DESCRIPTION

16       UGENE  is  a  cross-platform  environment  for DNA and protein sequence
17       analysis. UGENE integrates the  most  popular  bioinformatics  computa‐
18       tional  algorithms and provides both GUI and command line interface for
19       performing complex analysis of the genomic data.
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21       The main features of UGENE:
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23       *      View and analysis of annotated DNA or protein sequences
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25       *      Chromatograms visualization and editing
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27       *      Integrated 3D viewer for files in PDB and MMDB formats
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29       *      Integrated support of search requests to NCBI databases
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31       *      Multiple sequence alignment using MUSCLE3, MUSCLE4 and KAlign
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33       *      HMM profiles build and search, based on the source of HMMER2 and
34              HMMER3
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36       *      Modern  protein  secondary structure prediction algorithms based
37              on GORIV and PsiPred
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39       *      Phylogenetic analysis with Phylip
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41       *      PCR Primers design using Primer3 package
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43       *      Cloning in silico
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45       *      Search for transcription factor binding sites in  DNA  sequences
46              using SITECON
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48       *      Search for restriction enzymes and integration with REBASE
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50       *      Search for direct and invert repeats
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52       *      DNA reference assembly using Bowtie
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54       *      Protein back translation
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56       *      Search for ORFs
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58       *      Designer for complex computational workflows and queries
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61       UGENE  has  modular  structure  and  almost all its functionality comes
62       within plugins. Internally UGENE is designed with support of  parallel‐
63       ism  to make profit from using multicore computers. Every computational
64       task in UGENE is performed in background and does not block user inter‐
65       action with graphical interface.
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OPTIONS

69       -ui    run GUI version of UGENE
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71       --help print  a  usage  message  briefly  summarizing  all command-line
72              options and the program version, then exit.
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74       --license
75              dump license information
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77       --task=<path-to-schema or schema-name> [schema-options]
78              run given workflow schema
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80       --status-bar-hide
81              don't show task status bar
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83       --ini-file=<path-to-settings-file>
84              load custom UGENE settings file
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86       --log-no-show-level
87              don't show message level at log
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89       --log-no-show-date
90              don't show date&time info at log
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92       --log-no-show-category
93              don't show message category at log
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95       --log-level-trace
96              show trace log messages
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98       --log-level-none
99              don't show log messages
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101       --log-level-info
102              show error and info log messages (default)
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104       --log-level-error
105              show only error log messages
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107       --log-level-details
108              show details log messages
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110       --log-color-output
111              colored output messages
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113       --task-remote-machine=<path-to-machine-file>
114              run provided tasks on given remote machine
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116       --ugene-stay-alive
117              do not stop ugene after finishing given tasks
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119       --transl=<language-code>
120              load translations of specified language. Language  is  specified
121              as a two-letter ISO 639 language code
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COMMANDS

125       UGENE  has  commands for most significant features. Commands can be run
126       as
127              ugene <command-name> [command-arguments]
128              ugene --task=<command-name> [command-arguments]
129       See help for each command running ugene --help=<command-name>.
130       List of available commands can be dumped using ugene --help.
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BUGS

133       If you find a bug, please report it at ugene@unipro.ru.
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AUTHOR

137       ugene was created by Unipro (http://unipro.ru)
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142                               11 February 2011                       UGENE(1)