Substition Rate Using Ml And Paup

Question

[Smack The insect]

Hi,

i have an alignement file for which i'm using paup to deal with it.

i was able to generate the NJ tree, but i want to generate the Maximum Likelihood values for each specie along with the substitution rate for each site in the alignement (e.g C->T, ....)

i want to use the GTR model with gamma of 100

is this can be done using paup?? and how??

thank you

Answer 1

[Zev.Kronenberg]

If Paup can't do this I am pretty sure that Garli can.

[Smack The insect]

hi, is there any tutorial on how to use Garli to do this work (site specific substitution matrix for an aligment) ??

Answer 2

[SES]

I would suggest the program baseml that is part of PAML. This is what I have used and it is a widely accepted program for this task, but there are other methods to be aware of, for example BYPASSR (though I haven't tried this one).

[Smack The insect]

thank you, but can you guide me on how to use paup, paml or baseml to do this task, maybe a small intro. since i'm new to these programs

[SES]

When I read your question again I began to wonder whether PAML will do exactly what you need. If you are simply wanting to do a likelihood analysis on a phylogenetic tree then you should have look at RAxML: http://bodegaphylo.wikispot.org/RAxML_Tutorial. For reference, there is a brief tutorial on some of the PAML functionality here: http://molecularevolution.org/resources/activities/paml_activity and there is a good HOWTO wiki on the BioPerl site demonstrating how you can efficiently run and parse PAML output: http://www.bioperl.org/wiki/HOWTO:PAML. You will probably want to read over those pages and figure out which approach is most appropriate for your study.

[Smack The insect]

thank you, what i want to do is to get the substitution matrix for each position in the alinement (site specific substitution matrix) is this possible using PAML?? and is there any guide on how to do this??