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<p style="margin-top:0;margin-bottom:0">Thanks for the reply Thibaut.</p>
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<p style="margin-top:0;margin-bottom:0">I am actually just looking to generate some DNA sequences according to a given model of nucleotide substitution. </p>
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<p style="margin-top:0;margin-bottom:0">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. </p>
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<p style="margin-top:0;margin-bottom:0">haploGen/seqTrack appears to be the only such R function that generates DNA sequences automatically, given a pre-specified mutation rate of transitions. </p>
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<p style="margin-top:0;margin-bottom:0">I do have a followup question, as I am tweaking your implemented code to handle other evolutionary models:</p>
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<p style="margin-top:0;margin-bottom:0">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 </p>
<p style="margin-top:0;margin-bottom:0">Poisson(lambda = 1.5) distribution?</p>
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<p style="margin-top:0;margin-bottom:0">Thanks. </p>
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<p style="margin-top:0;margin-bottom:0">- Jarrett</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Thibaut Jombart <thibautjombart@gmail.com><br>
<b>Sent:</b> Monday, August 20, 2018 9:27:30 AM<br>
<b>To:</b> Jarrett Phillips<br>
<b>Cc:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [adegenet-forum] Nucleotide substitution model used by haploGen()/SeqTrack()</font>
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<div dir="ltr">Hi Jarrett
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<div>if this is something you want to use for reconstructing transmission trees, I would recommend using a more advanced method such as outbreaker2 (<a href="http://www.repidemicsconsortium.org/outbreaker2/">http://www.repidemicsconsortium.org/outbreaker2/</a>)
as SeqTrack was a very crude first pass at that problem. </div>
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<div>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.</div>
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<div>Best</div>
<div>Thibaut <br clear="all">
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<div><font face="arial, helvetica, sans-serif" size="1"><br>
--<br>
Dr Thibaut Jombart<br>
Senior Lecturer in Genetic Analysis, Imperial College London</font></div>
<div><font face="arial, helvetica, sans-serif" size="1">Associate Professor in Outbreak Analytics, London School of Hygiene and Tropical Medicine<br>
Head of RECON: <a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a></font></div>
<div><font face="arial, helvetica, sans-serif" size="1"><a href="https://thibautjombart.netlify.com" target="_blank" style="letter-spacing:0.2px">https://thibautjombart.netlify.com</a><br>
</font></div>
<div><font face="arial, helvetica, sans-serif" size="1">Twitter: @TeebzR<br>
+44(0)20 7594 3658</font></div>
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<div class="x_gmail_quote">
<div dir="ltr">On Fri, 17 Aug 2018 at 14:16, Jarrett Phillips <<a href="mailto:jphill01@uoguelph.ca">jphill01@uoguelph.ca</a>> wrote:<br>
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My inquiry concerns seqTrack(), which employs haploGen() to simulate a haplotype genealogy through time. </div>
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haploGen() generates DNA sequences under a Kimura-2-Parameter substitution model with equal base frequencies and differing transition/transversion rates.</div>
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<b>My question is</b>: 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. </div>
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Trying this approach for each of standard and mitochondrial codon tables seems to give conflicting results as to the best substitution model.</div>
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<font size="3"><span style="font-size:12pt">Could someone shed some light on this? I would appreciate</span></font><font size="3"><span style="font-size:12pt"> any insight one might be able to </span></font><font size="3"><span style="font-size:12pt">offer.</span></font></div>
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Thanks.</div>
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