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tutorials:eccb_t2_diverge [2012/09/06 20:27] romainstuder |
tutorials:eccb_t2_diverge [2012/09/07 16:47] (current) romainstuder |
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| There is a self-extracting archive at this website: | There is a self-extracting archive at this website: | ||
| http://xungulab.com/software/diverge2/diverge2.html | http://xungulab.com/software/diverge2/diverge2.html | ||
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| + | 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. | ||
| + | |||
