Dear Zhuocheng,
Quote:I want to test the variable dn/ds values for the background and also for the foreground. I had lots of gene to test. So, I need to write scripts for the automated processing multiple alignment. As you said, you had wrote these scripts. Can you find it?
I'll post a link on Friday; I am currently away from my office
Quote:Another question is how to make test on the specific branch or node by using the script in the automated processing script? I don't know whether I can provide the use defined tree. Actually, I must provide the user defined tree topology and test the selection on the specific branch/node.
You could automate the process, because HyPhy prompts (you can feed in data non-interactively as well) for the branch (es) to test. The only problem arises if you have different sequence (and tree leaf) names in different alignments, or if you want to test an interior lineage but topologies differ between trees. I need more information about your analysis to tell you how to proceed.
Quote:Third question is how about the performance of the HyPhy to test the purifying selection on the specific lineage? How can I perform it in the HyPhy script?
The same test can be used, except with a different one-sided constraint (dN<dS instead of dN>dS).
Cheers,
Sergei