
                           ----------------
                            UNIPRO   UGENE
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What is it?
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Unipro UGENE is a free unified bioinformatics toolkit. 
The goal of the project is to integrate popular bioinformatics
methods and algorithms within single visual interface. 

UGENE allows to construct custom analisys pipelines using powerful
extension named Workflow Designer. These pipelines could be used as
individual command line tools.

UGENE main features:
* Multiple sequence alignment using MUSCLE 3 and KAlign;
* HMM profiles build and search, based on the source of HMMER;
* PCR Primers design using Primer 3;
* Protein secondary structure prediction using GOR IV and PSIPRED;
* Phylogenetic analysis with Phylip;
* Search for restriction enzymes and integration with REBASE;
* Extremely fast repeat finder;
* DNA reference assembly using Bowtie;
* Search for transcription factor binding sites using SITECON;
* Protein back translation;
* ORF finder;
* Complete Smith-Waterman algorithm implementation;
* Comparing genomes using dotplot view. 

UGENE is licensed via GPLv2.

Please, visit http://ugene.net for more details.


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Install and setup environment
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You can launch UGENE right away from the unpacked binary snapshot directory.

To make UGENE available from any location on your machine 
add the following lines to your .bash_profile:

export PATH=$PATH:/path/to/ugene/
export MANPATH=$MANPATH:/path/to/ugene/


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Running UGENE
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The GUI version:
./ugene -ui

Command line version:
./ugene 


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Documentation
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There is man page available for command-line version:
man man1/ugene.1.gz

For complete user documentation visit:
http://ugene.net/manual


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Directory structure
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README  This file

ugene  UGENE executable script

man1/   UGENE man page dir

plugins/  Plugins dir

ugenecl UGENE console executable file

ugeneui UGENE GUI executable file

data/  Sample data for supported formats, workflow samples, weight matrices, 
       DNA back translation tables, enzymes data, list of known remtote databases etc.

*.so.4 Shared libraries required by UGENE

*.qm  Translations of UGENE to various languages






