Re: [CDAO-discuss] Seeking list of nucleotide substitution models

[Hilmar L. <hl...@ne...>]

This is from a post to R-SIG-phylo. What do folks here think about using the following part of the Jmodeltest2 documentation for fleshing out the substitution models section in CDAO?

https://code.google.com/p/jmodeltest2/wiki/TheoreticalBackground#Hierarchical_Likelihood_Ratio_Tests_(hLRT)

Daniel - while not the kind of answer you were hoping for, I'd be very appreciative if you could forward to me if you do receive pointers to good sources. FYI, CDAO is the Comparative Data Analysis Ontology (http://www.evolutionaryontology.org/).

	-hilmar

On Apr 5, 2013, at 12:23 PM, Daniel Barker wrote:

> 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
> 
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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