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tutorials:eccb_t2_diverge [2012/09/06 16:44]
romainstuder created 		tutorials:eccb_t2_diverge [2012/09/07 16:47] (current)
romainstuder
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 +== 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 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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