Hi,
Could someone please tell me the exact definition of "dna pattern site" in raxml? Or at least, what we mean by that?
Thanks a lot
Hi,
Could someone please tell me the exact definition of "dna pattern site" in raxml? Or at least, what we mean by that?
Thanks a lot
Site pattern
isn't a concept from RAxML alone, it is a general concept in phylogeny. Alignments are used to infer site patterns, and actual likelihood (or Bayesian) calculations are performed over site patterns.
The clearer definition I could find is from Rhiju Das dissertation - see section "2.1. Likelihood basics.", at page 6:
Explicitly, a site pattern is defined as a set of molecular characters that exist at a given site in the taxa.
Probably good phylogeny books will have the definition, but I don't have one at hand to check.
edit: read the PAML documentation, it explains how to convert / represent an alignment as site patterns.
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