[adegenet-forum] Nucleotide substitution model used by haploGen()/SeqTrack()

[Thibaut Jombart]

Hi Jarrett

if this is something you want to use for reconstructing transmission trees,
I would recommend using a more advanced method such as outbreaker2 (
http://www.repidemicsconsortium.org/outbreaker2/) as SeqTrack was a very
crude first pass at that problem.

As for the substitution model, in outbreak reconstruction is usually
doesn't matter. But if you are doing phylogenetic reconstruction then I
would use the usual ML / likelihood ratio tests to compare different models
in phangorn. AIC / BIC should hopefully give similar results.

Best
Thibaut

--
Dr Thibaut Jombart
Senior Lecturer in Genetic Analysis, Imperial College London
Associate Professor in Outbreak Analytics, London School of Hygiene and
Tropical Medicine
Head of RECON: repidemicsconsortium.org
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658


On Fri, 17 Aug 2018 at 14:16, Jarrett Phillips <jphill01 at uoguelph.ca> wrote:

> My inquiry concerns seqTrack(), which employs haploGen() to simulate a
> haplotype genealogy through time.
>
> haploGen() generates DNA sequences under a Kimura-2-Parameter substitution
> model with equal base frequencies and differing transition/transversion
> rates.
>
> *My question is*: how can we be certain that the sequences really
> do conform to a K2P model? Since these are simulated data, it would be
> difficult to choose the most parsimonious model based on the BIC (using
> MEGA software for instance), as one is required to select the appropriate
> codon table (e.g., standard vs. mitochondrial), to ensure proper placement
> of STOP codons.
>
> Trying this approach for each of standard and mitochondrial codon tables
> seems to give conflicting results as to the best substitution model.
>
> Could someone shed some light on this? I would appreciate any insight
> one might be able to offer.
>
> Thanks.
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