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heterochronous sequences (rates & dating) (Read 3475 times)
sergios-orestis
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heterochronous sequences (rates & dating)
May 21st, 2006 at 11:30am  
Dear Sergei,

I was wondering if there was a bf to get substitution rates and divtimes from heterochronous sequences, similar to BEAST (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login) - using a global clock or relaxing it.

Would your TipDate-type bf do the job? I read the two TipDate-related posts, but you say "dated contemporaneous sequences" - do you mean that your TipDate bf estimates MRCA dates from contemporaneous sequences or you just meant "non-contemporaneous" instead? If it's the latter, would it be possible to get substitution rates, brlengths and proceed to a RR test?

Congrats for such a great program (and server)!

Thanx for your time,
sergios
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Sergei
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Re: heterochronous sequences (rates & dating)
Reply #1 - May 21st, 2006 at 10:12pm  
Dear Sergios,

I did mean to say dated NON-contemporanous sequences. That analysis is effectively an updated and more model-rich version of the global clock test a-la TipDate. We have some 'beta' Genetic Algorithm analyses which can do the test allowing a relaxed clock (i.e. multiple rates). Let me know if you are interested and I can e-mail you the files. Eventually (in the next month or so), I am actually going to add dating type analyses to datamonkey.org as well.

Cheers,
Sergei
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sergios-orestis
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Re: heterochronous sequences (rates & dating)
Reply #2 - May 23rd, 2006 at 11:20am  
Dear Sergei,

thank you for your reply. Yes, I'd be interested to check out the relaxed TipDate-type bf.

Is there a readme for the TipDate bf (input file, how to get substitution rates, MRCA divtimes)? I think I saw something on a post some time ago, but I can't seem to find it.

Thanks again,
sergios
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Sergei
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Re: heterochronous sequences (rates & dating)
Reply #3 - May 31st, 2006 at 4:40pm  
Dear Sergious,

I updated the DatedTipsMolecularClock.bf file. It'll be rolled into the next build; in the meantime, you can download (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login) and run it in the current version of HyPhy. File input are normal sequence data, with TipDate style node dates (or embedded branch lengths) - take a look at examples given in the prompts. The analysis outputs everything - rates, MRCA and internal node dates, confidence intervals, and dated clock p-values - to the console and graphically automatically.

Cheers,
Sergei
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