How Can I Use Paml To Calculate The Dn/Ds Value Of Only Some Specific Branches?

Question

[cacaucenturion]

Since it often takes a long time to calculate the dN/dS value of a big tree, how can I calculate the value only for some branches? Thanks!

Answer 1

[Botond Sipos]

You can use a branch model (model = 2) and assign an omega parameter to the branch(es) of interest and a common omega to all other branches. It should be faster than calculating different omegas for every single branch (model = 1). Check out the PAML documentation for the details.

Answer 2

[Kartik Sunagar]

I suggest trying the Branch-site REL implemented on datamonkey instead. I strongly recommend not using the free-ratio model since it is very parameter rich and is discouraged by the author of the software itself.

Answer 3

[figo]

It depends on what you want to achieve ? What kind of test you want to do?. There are basically two types of tests if you are interested on some specific branches in tree one is the branch specific test and the other is the branch site test. You can see the details in the PAML manual for setting the parameters in the .ctl file. The branches which you want to test will be just needed to be changed in the tree file using a hash (#). If you simply wants to know the omega values on all the branches then you should run the free ratio test but it is parameter rich and you should avoid this.