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Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguity characters
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17 months ago
Denis • 70

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!

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17 months ago
Klaus S • 100

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")
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