Added tutorial page

docs/index.rst

@@ -14,6 +14,7 @@ Contents:
    tcoffee_quickstart
    tcoffee_installation
    tcoffee_manual
+   tcoffee_tutorials
    tcoffee_faq
    tcoffee_reference
    trmsd_manual

docs/tcoffee_tutorials.rst

@@ -0,0 +1,47 @@
+*******************
+T-Coffee Tutorials
+*******************
+
+Using the T-Coffee Package to Build Multiple Sequence Alignments of Proteins, RNAs, DNA 
+sequences and 3D-Structures.
+
+Introduction
+---------------
+
+T-Coffee is a versatile Multiple Sequence Alignment method suitable for aligning most types 
+of biological sequences. The series of protocols presented here show how the package can be 
+used to multiply align proteins, DNA and RNA sequences. 
+
+The protein section presents controlled cases for PSI-Coffee the homology extended mode suitable 
+for remote homologues, Expresso the structure based multiple aligner and M-Coffee, a meta-version 
+able to combine several third party aligners into one. 
+
+We then show how the T-RMSD option can be used to produce a functionally informative structure 
+based clustering. RNA alignment procedures are shown for R-Coffee a mode that produces secondary 
+structure based MSAs. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific 
+of promoter regions. The last sections presents the many reformatting utilities bundled with T-Coffee. 
+
+The package is an open-source freeware available from `www.tcoffee.org <http://www.tcoffee.org>`_.
+
+
+Materials
+-----------
+
+The list of files (input and output) required by this protocol is available 
+from `here <http://www.tcoffee.org/Packages/NatureProtocols/NatureProtocolDataset.tar.gz>`_. 
+
+They can be automatically retrieved using the following command::
+
+    t_coffee -other_pg nature_protocol.pl    
+
+This will create 4 repertories containing the input sequences necessary for the protocols 
+we report in this section. For each part, all command lines have been collected into the file README.sh.
+
+Procedures
+------------
+
+- Installation
+- Protein Multiple Sequence Alignments
+- RNA Multiple Sequence Alignments
+- Promoter alignments
+- Reformat alignments