raxml - definition of site

Question

[estranged22]

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

Answer 1

[h.mon]

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.