Nucleotide sequence simulation

Andrew Rambaut andrew.rambaut at zoo.ox.ac.uk_remove_this_
Thu Jul 5 05:52:48 EST 2001


in article 9hvjhe$3pd$1 at mercury.hgmp.mrc.ac.uk, Anders Gorm Pedersen at
gorm at cbs.dtu.dk wrote on 4/7/01 6:25 PM:

> I think you night find Hidden Markov Models (HMMs) to be useful for this
> kind of thing. Briefly this type of model can be estimated ("trained") on a
> set of aligned sequences, and then used in "generative mode" to produce
> sequences having the same characteristics as the aligned set. I've included
> a few pointers below. The HMM packages HMMER (pronounced "hammer") and SAM
> are free for academic users but only run on UNIXes. HMMpro is also free for
> academic users and runs on some unix flavors and also on Windows NT.

How do these models deal with phylogeny? Does the model estimate the
phylogenetic relationships between the sequences or assume independent
lineages (or some sort of pair-wise relationship)?

Andrew

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