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Question: Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguity characters
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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 9 months ago Denis • 70 • updated 8 months ago Klaus S • 100
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The function in the R package phangorn handles ambiguity characters like they are handled in ML optimisation.

dat <- read.phyDat("msa.fas", format="fasta), model = "F81", exclude = "none")
ADD COMMENTlink 8 months ago Klaus S • 100

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