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[GradMom]

I'm new to PAML and phylogenetic analysis in general.  I'm running a bunch of alignments through PAML to calculate dN/dS per branch and I need to give it a species tree but I'm not familiar with the parenthetical notation it requires.  Can anyone help me out?

The species I'm using are:
Human, Chimp, Orangutan, Gorilla, Mouse, Rhesus Macaque, & Cow

Thanks!

[Hamish McWilliam]

That sounds like the Newick tree format. The Newick format article in Wikipedia provides a good explaination of the format.