Dear George
after all this useful background information from Joe, Brian et al. back to
your initial question, if it is still valid by now. Yes, you can use pml
for this. You actually do not have to mess with the pml function itself.
As nucleotides, amino acids, codons etc. are discrete phyDat ob
You might want to take a look at this paper: PLoS One. 2014 Jul
17;9(7):e102857. doi: 10.1371/journal.pone.010285
to see how we handled experimental error based on phred values.
This could be used in combination with all the other suggestions, of course
(in fact it will be interesting to compare t
Brian O'Meara added:
> Something like that should work. Unlike the case of ambiguity, where if you
> see, say, a Y at a site you'd give the probability of a C or a T at that
> site each 1, not 0.5 (Felsenstein's book has a good discussion of this) I
> think you're right that you'd want the probab
George Shireff asked:
>
> I was wondering if there is a way to incorporate sequencing error in
> phylogenetic analysis, if I know there is sequencing error but it's
> randomly distributed.
>
> I imagine this could be as simple as setting the probability of the
> observed base at each tip to 0.99 r
Something like that should work. Unlike the case of ambiguity, where if you
see, say, a Y at a site you'd give the probability of a C or a T at that
site each 1, not 0.5 (Felsenstein's book has a good discussion of this) I
think you're right that you'd want the probabilities to add up to one
across
Hello,
I was wondering if there is a way to incorporate sequencing error in
phylogenetic analysis, if I know there is sequencing error but it's
randomly distributed.
I imagine this could be as simple as setting the probability of the
observed base at each tip to 0.99 rather than 1, with a probabi
