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--- tutorials:eccb_t2_diverge [2012/09/06 16:44] – created romainstuder
+++ tutorials:eccb_t2_diverge [2012/09/07 16:47] (current) – romainstuder
@@ Line 1: / Line 1: @@
+== Diverge2 ==
-Diverge2:
+There is a self-extracting archive at this website:
-There is a self-extracting archive on the website:
 http://xungulab.com/software/diverge2/diverge2.html
+We want to analyse the GAPDH family.
+Dowload the following files (alignment and 3D structure), unzip them and load them into Diverge2:
+   * {{:tutorials:gapdh_alignment.fasta.zip|}}
+   * {{:tutorials:2pkq.pdb.zip|}}
+In the "Clustering" tab, select "NJ Tree-Making", "Kimura" method (but you can also produce a tree with ML methods and load it).
+  * Click on the node at the basis of group C, and reroot the tree.
+  * Click on the node at the basis of group C, and "Add cluster" => Name "GapC".
+  * Click on the node at the basis of group A, and "Add cluster" => Name "GapA".
+In the "Gu99" tab, click on calculate. Could take time. It produce the score for the original Type I of functional divergence.
+In the "Gu2001" tab, click on calculate. Could take time. It produce the score for an updated Type I of functional divergence.
+In the "Type II Divergene" tab, click on calculate. Could take time. It produce the score for the  Type II of functional divergence.
+When you click on a column, you can visualise the posterior probability per site.
+The visualisation on the multiple seems to cause the program to crash. So use Jalview instead.

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