Open mlosilla opened 3 years ago
Dear @mlosilla,
@SVMuse reads these, boards once in a while, so maybe he can chime in.
Best, Sergei
Hi Sergei,
Thank you for your reply and links, and it is much clearer now. A couple of follow-ups:
1) My goal with these data is to make a figure of my phylogeny with branch lengths: a) proportional to either "non-synonymous" or "non-synonymous" + "synonymous", I haven't decided which, and b) color-coded with a heatmap of the dN/dS ratios (w).
For 1b) the correct value would be the MLE right?
2) some MLE estimates are very high, probably due to a lack or almost lack of synonymous substitutions. How are those best interpreted?
3) more of a theoretical question: How does the taxonomic breadth of the phylogeny influence the w estimates? Does the Inclusion of more distantly related clades usually tends to affect dN and dS differently?
Thanks Mau
Hi,
I am trying to understand the output of the FitMG94 model with per branch calculation (--type local).
For example, the output for one node is:
"Node20":{ "Confidence Intervals":{ "LB":0.05288894421311353, "MLE":0.1201576050549771, "UB":0.2263100014412389 }, "Nucleotide GTR":0.04948062317408397, "Standard MG94":0.05264881492703954, "dN":0.01794621524493222, "dS":0.1586217234027807, "nonsynonymous":0.01351914523388944, "original name":"Node20", "synonymous":0.03912966969315013
Is the following correct:
MLE is the estimation of dN/dS = w, and it has a confidence interval with lower bound (LB) and upper bound (UB) limits, estimated by "profile likelihood" (I found this phrase in another post)
"synonymous" and "nonsynonymous" are the values used in the synonymous and non-synonymous trees. These are the number of synonymous and non-synonymous substitutions per codon, and also the branch lengths. Could the total branch length be computed as "synonymous" + "nonsynonymous"?
dN and dS are the number of [non]-synonymous substitutions divided by the number of codons that display [non]-synonymous substitutions in the alignment ???
Is w (MLE) calculated (or very closely approximated) by dS/dN?
Thanks Mau