PAML

Jason Stajich jason.stajich at NOSPAMBOTS-duke.edu
Fri Sep 5 12:35:21 EST 2003


sdann at uvic.ca wrote:
> Can anyone instruct me on how to use this software. I am totally lost!
> 
> 
> http://biowww.net/mynews/tree.php?group_name=bionet_software&begin=0

Your link doesn't work for me but the PAML website is
http://abacus.gene.ucl.ac.uk/software/paml.html

There is a manual as well as many example files provided in the 
distribution illustrating a number of different questions you can ask 
and the various input file formats which are supported.

We've built perl wrappers about it in bioperl www.bioperl.org for 
automating the running of many analyses at a time, but if you are just 
running a few datasets it makes more sense to run it manually.

--jason





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