Hi Sergei,

I am new at this and would greatly appreciate if you check my code. I have two aligned sequences and i want to test whether the three codon sites evolve at equal rates.

I have attached my code


  Thank you

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Hi Nick,

Your code looks good, apart from the fact that comments in HyPhy are C-style ( '//' or '/* */' ), and not Perl (#) style.
One minor point is that in your code, the branch lengths are still slightly different even AFTER you constrain 'b', because the base frequencies are different among partitions.

You could uses pooled base frequencies among all partitions (i.e. the same HKY85 model) which doesn't have this issue; if you need to maintain different sets of frequencies, some transformations of 'b' are required (see the attached file).

Sergei

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