Phylogenetic Analysis By Maximum Likelihood (Paml)

Question

[Naren]

Has anybody tried Phylogenetic Analysis by Maximum Likelihood (PAML) in Windows.
How to calculate omega for many bacteria of same species to check positive selection?
I didn't get it through their manual.
What commands should be given through cmd.

[Damian Kao]

We need some more information. What have you tried and what errors are you getting?

[Naren]

Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.

Answer 1

[aidan-budd]

The instructions you need to follow, to run PAML programs under windows, are found here:

http://abacus.gene.ucl.ac.uk/software/paml.html

You need to read the section "Downloading and Setting up PAML" and then subsection "Windows 9x/NT/2000/XP/Vista/7"

This info may be missing from the manual, so have a go at looking through this stuff if you've not tried it already.

Note that there is no "program" called "paml" or "PAML", rather you run individual programs within the PAML packaged (in your case it would be codeml)

I've never used PAML under windows, but I think the idea is the same as under *nix i.e. the instructions about which data file to use, and which paramenters to run the analysis with, are specified in a "control" file that you set up (and give an appropriate name to) prior to running the programs

[Naren]

@aidan Thank you for the response. codeml is running. My doubt is that do we need to modify control file every time. What format should be the input?

[aidan-budd]

It depends. Probably you do need to modify the control file each time, otherwise you will always be running codeml with the same input file (name) and output file (name) - although I guess you could run a pipeline where you:

• set up infile and outfile name in the control file

• provide approrpiate infile content

• run codeml

• rename outfile to an appropriate name

• provide codeml with differnet input by renaming a file to the name of the infile in your control file

• run codeml

• repeat

This way you could process a set of different datafiles using the same set of parameters, without having to edit the control file each time

[Naren]

@aiden-budd: see this question. link : Phylogenetic Analysis By Maximum Likelihood (Paml) : Upon Phylip Input Yn00.Clt Program Not Running.