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

Thibaut Jombart thibautjombart at gmail.com
Mon Aug 20 15:27:30 CEST 2018

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.


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
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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