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update of the tutorial doc section
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cnotred committed Dec 10, 2015
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Expand Up @@ -5,6 +5,9 @@ T-Coffee Tutorials
Using the T-Coffee Package to Build Multiple Sequence Alignments of Proteins, RNAs, DNA
sequences and 3D-Structures.

This documentation is merely a cheat-sheet that recapitulates the material and the command-lines associated with the tutorial.
The tutorial itself is adpated from the `T-Coffee Nature Protocol Article <http://www.nature.com/nprot/journal/v6/n11/full/nprot.2011.393.html>` that can be followed step by step on the following site: `Online T-Coffee Tutorial <http://www.tcoffee.org/Projects/tcoffee/workshops/tcoffeetutorials/index.html>`

Introduction
---------------

Expand Down Expand Up @@ -40,8 +43,8 @@ we report in this section. For each part, all command lines have been collected
Procedures
------------

- Installation
- Protein Multiple Sequence Alignments
- RNA Multiple Sequence Alignments
- Promoter alignments
- Reformat alignments
- `Installation <http://www.tcoffee.org/Projects/tcoffee/workshops/tcoffeetutorials/installation.html>`
- `Protein Multiple Sequence Alignments <http://www.tcoffee.org/Projects/tcoffee/workshops/tcoffeetutorials/protein-alignment.html>`
- `RNA Multiple Sequence Alignments <http://www.tcoffee.org/Projects/tcoffee/workshops/tcoffeetutorials/rna-alignment.html>`
- `Promoter alignments <http://www.tcoffee.org/Projects/tcoffee/workshops/tcoffeetutorials/promoter-alignment.html>`
- `Reformat alignments <http://www.tcoffee.org/Projects/tcoffee/workshops/tcoffeetutorials/reformating.html>`

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