Best hyphy tool for estimating synonymous nucleotide substitution rates / divergence

[siribi]

Hi,

Thank you for developing such a great software package. We are interested in using HyPhy not to detect selection, but to estimate synonymous nucleotide substitution rates (i.e., only dS) between branches. Could you recommend the most suitable tool for this purpose?

We noticed that the SLAC output file includes a field described as "synonymous substitution count, the number of synonymous substitutions per site inferred to have occurred along this branch." Would SLAC be the best choice for our needs, or is there another tool within HyPhy that you would recommend?

Our alignments are small - only six sequences from different subspecies.

Best regards,
S

[spond]

Dear @siribi,

I would use FitMG94, e.g see #1573

Best,
Sergei

[siribi]

Thank you so much, Sergei! - And sorry for double posting!

Best,
Siri

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