Question: Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguity characters
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gravatar for Denis
6 months ago by
Denis140
Denis140 wrote:

I have a nucleotide multiple sequence alignment (MSA) with many IUPAC ambiguity characters like W,S,R, etc. I need to calculate distance matrix for making phylogenetic tree (as next step), but i'd like that all nucleotides (including ambiguity characters) would be taken into account during distances calculation. Is there any solution for my case. Thanks!

ADD COMMENTlink modified 6 months ago by Klaus S100 • written 6 months ago by Denis140
2
gravatar for Klaus S
6 months ago by
Klaus S100
Klaus S100 wrote:

The function dist.ml in the R package phangorn handles ambiguity characters like they are handled in ML optimisation.

library(phangorn)
dat <- read.phyDat("msa.fas", format="fasta)
dist.ml(dat, model = "F81", exclude = "none")
ADD COMMENTlink written 6 months ago by Klaus S100

Thanks! As i understand F81 model is four parametric in typical case. I'm wondering if it would have much more parameters in case of IUPAC ambiguity characters? It will extract the base frequences from the nucleotide alignment, which i'm using as input. Am i right?

ADD REPLYlink written 5 months ago by Denis140
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