Hi,

I would like to simulate sequences with a user-defined tree, branch lengths and omega specific for each branch. The idea is to simulate the sequences and then re-estimate the omega and see if HyPhy (and PamL) can correctly estimate the omega.

I can do this in INDELible specifying the codon frequency matrix, is there a similar way of doing it in HyPhy (using GUI)? Or any other way that lets me control the GC content of the sequences?

Thanks!
Fabia