Dear Sunil,

BranchAPriori is an options when you run Miscellaneous->Phylonandbook.bf
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Speaking of data dredging, you should NOT fit the local model, identify which branches have dN>dS and test those using other models. The test will be biased to find significance (because you use the same data to generate a hypothesis and then test it). One way to get around this is to use a low p-value (e.g. 0.05/number of branches); that would effectively enforce a Bonferroni correction as if you tested every single branch one at a time. Another is to use a GA, where you don't define what is your model a priori but simply let the GA find which ones fit well.

HTH,
Sergei

Dear Sunil,

1. Try opening your alignment in HyPhy (File->Open->Open Data File) and see if the tree is recognized.
Two possibilities why your tree is not read are: some leaf names do not match sequence IDs, or that the tree is simply not recognized.

2. GA branch returns a model averaged confidence set of what the dN/dS for the branch may be. You should use this distribution, not a single dN/dS value.

3. Branch partition files are currently only recognized by Compartmentalization>BranchClassDNDS.bf. Nielsen-Yang's branch site methods are set up to only permit two partitions of branches (foreground and background). You can select which ones are in the foreground manually.

HTH,
Sergei