Question regarding SNP alignment input

[mstagliamonte]

Dear authors,

I am trying generate a time tree by using an informative-only alignment, and, after reading the manual, I need some advice. in addition, since I am dealing with M. tuberculosis sequences, I would need to use a pre-set clock (1.1e-7). I see that when running an homoplasy, I can add --resscale and --const parameters; however, these are not usable in the estimation of a time tree.

I was wondering how I can go around that; should I just rescale the evolutionary rate to the alignment length? i.e., with a 223 sites alignment, I would rescale as following:

1.1e-7 * 4.4Mb/223 = 0.002

Or do I necessarily need to use a vcf input?

Best,
Max