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Diverge2
There is a self-extracting archive at this 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:
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.
