Can you tell me hyphy does with missing sequence data? I have about 20kb of sequence from 7 species, but in ~5% of the data 1 species will be missing (it's an N in the sequence)

What does HYPHY do with this? Does it ignore those columns? Or does it just give that branch a likelihood of 1 (integrating over the unknown data)? Ideally, I won't exclude these columns.

Also, Hyphy ignores columns with indels, right?

thanks,
scott

Dear Scott,

HyPhy (by default) will treat ambiguities (or N,?,- etc) as (partially or fully) missing data - i.e. having an 'N' at a tip in the tree at a site is equivalent to computing the likelihood at the site on a reduced tree where all branches with 'N' have been pruned.

If you take a look at pages 5-6 in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login, this is explained in more detail.

Cheers,
Sergei

P.S. Doesn't seem like a bug report to me, so I'll move the thread to 'Feedback'