Hi,

I'm building 4 taxon trees using fairly short alignments and I want to test whether one or more branches are under differing selection pressures. I have about 100,000 alignments to test and each is built from a single species' perspective.

I have therefore started by looking at using TestBranchDNDS.bf to test whether my starting sequence (which is my key interest) is under a different selection pressure than the rest of the tree. However I don't understand one of the options, the nsClass2 or nsClass1 rate parameter. What are these parameters and how will they affect the result? Also for those alignments where I get a significant result how do I tell if this branch is under positive or negative selection?

The alignments I am keen to locate from my dataset would hopefully show two of the species to be under negative selection (the genes are under constraint) while a third species has a more positive selection as the constraint has been released. I'm therefore weary of comparing my branch of interest against a global background if I suspect that background could comprise these different rates. Is there therefore a more appropriate test I could use?

I've read through the HyPhy book as well as other posts and papers and I can't seem to find an answer to my questions so I hope you can help,


Thanks,

Teri

Sergei,

Thanks for the suggestion, so far it seems to be working but it is a little slow. How do I tell HYPHYMP to use multiple threads? I was expecting to add an argument when I start the program using my batchfile but I can't find any documentation about what to add,

Thanks for the help,

Teri