Hi Daniel, Have you looked at the help page of dist.dna? The list of references there is focused on calculating distances but some are general. There are a few more references in my book too. I suggest you also look at "Inferring Phylogenies".
Best, Emmanuel -----Original Message----- From: Daniel Barker <d...@st-andrews.ac.uk> Sender: r-sig-phylo-boun...@r-project.org Date: Fri, 5 Apr 2013 16:23:36 To: r-sig-phylo@r-project.org<r-sig-phylo@r-project.org> Subject: [R-sig-phylo] Seeking list of nucleotide substitution models Hello, Is there a review or list of ~every specific nucleotide substitution model that has been proposed or used in the literature (with references)? I'm interested in reversible models. The most exhaustive list I have is from the jModeltest documentation, https://code.google.com/p/jmodeltest2/wiki/TheoreticalBackground#Models_of_ nucleotide_substitution I realise an enormous number of models is possible (and may have been used in model averaging). I'm keen to know which have some precedent in the literature, along the lines of those listed above. I'm finding it difficult to get beyond the standard sources. Thank you in advance, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
