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* Multiple sequence alignment - SeqAn::T-Coffee *
* (c) Copyright 2009 by Tobias Rausch           *
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Table of Contents
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  1.   Installation
  2.   Example
  3.   Contact
  
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1. Installation
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SeqAn::T-Coffee is distributed with SeqAn, http://www.seqan.de. 
You can build it using the latest snapshot or directly from
the SVN repository.

Snapshot:

  1)  Download the latest snapshot of SeqAn
  2)  Unzip it to a directory of your choice (e.g. snapshot)
  3)  cd snapshot/apps
  4)  make seqan_tcoffee
  5)  cd seqan_tcoffee
  6)  ./seqan_tcoffee --help

SVN:

  1)  svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan
  2)  cd seqan
  3)  make forwards
  4)  cd projects/library/apps
  5)  make seqan_tcoffee
  6)  cd seqan_tcoffee
  7)  ./seqan_tcoffee --help

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2. Example
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Accurate protein alignment:
./seqan_tcoffee -s seq.fa
./seqan_tcoffee -s seq.fa -f msf

Fast protein alignment:
./seqan_tcoffee -s seq.fa -m local

DNA alignment:
./seqan_tcoffee -s seq.fa -a dna

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3. Contact
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For questions or comments contact:
  Tobias Rausch <rausch@inf.fu-berlin.de>
