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

[Thibaut Jombart]

I am not sure I understand the question. Each haplotype is, by definition,
one sequence. I assume we are talking about the number of descendants for a
given haplotype in the simulation. If so, you are right, the number of
descendants is determined by the function 'repro', which defaults to:
function(){rpois(1,1.5)}

Then for each descendant:
- the time of evolution since the ancestral sequence is determined
- transitions and transversions are determined
- resulting sequences are output

Does it make sense?
Best
Thibaut



On Mon, 20 Aug 2018 at 19:53, Jarrett Phillips <jphill01 at uoguelph.ca> wrote:

> Thanks for the reply Thibaut.
>
>
> I am actually just looking to generate some DNA sequences according to a
> given model of nucleotide substitution.
>
>
> I opened a GitHub issue for the adegenet repository a few weeks ago, which
> was handled by Emmanuel Paradis, expressing my interest in being able to
> simulate DNA sequences without having to specify a phylogenetic tree as
> input. As I understand, the majority of R packages require a tree in order
> to simulate DNA sequences along branches.
>
>
> haploGen/seqTrack appears to be the only such R function that generates
> DNA sequences automatically, given a pre-specified mutation rate of
> transitions.
>
>
> I do have a followup question, as I am tweaking your implemented code to
> handle other evolutionary models:
>
>
> How exactly is the number of DNA sequences to be contained in each
> haplotype specified? Is this done with the repro() function in haploGen?
> That is, is the number of DNA sequences for each haplotype generated
> according to a
>
> Poisson(lambda = 1.5) distribution?
>
>
> Thanks.
>
>
> - Jarrett
>
>
> ------------------------------
> *From:* Thibaut Jombart <thibautjombart at gmail.com>
> *Sent:* Monday, August 20, 2018 9:27:30 AM
> *To:* Jarrett Phillips
> *Cc:* adegenet-forum at lists.r-forge.r-project.org
> *Subject:* Re: [adegenet-forum] Nucleotide substitution model used by
> haploGen()/SeqTrack()
>
> 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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