Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender: Re: Site specific rate estimation (SiteRates.bf) Reply #5 - Jan 4th, 2007 at 11:03am   Dear Travis,You should NOT use the tree output by HyPhy to determine the total tree length, because that length is the product of (mean rate)*evolutionary_time, hence normalizing your site-specific rate estimate by this length will result in Code:(site rate)/((mean rate) * (evolutionary time)) .Site rates, as output by HyPhy, are relative to the 'mean' (not necessarily average, I use this term loosely) rate for the entire alignment, and can only be compared to each other. Because all sites in the same gene (most likely) evolved for the same duration of time, this comparison is meaningful. If you have some other means of estimating tree lengths (e.g. based on molecular clock), then you can divide out the time.What are some of the oddities you are seeing?Hope this helps.Cheers,Sergei Back to top Associate ProfessorDivision of Infectious DiseasesDivision of Biomedical InformaticsSchool of MedicineUniversity of California San Diego IP Logged