Question: Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguity characters
1
gravatar for Denis
17 months ago by
Denis200
Denis200 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 16 months ago by Klaus S140 • written 17 months ago by Denis200
6
gravatar for Klaus S
16 months ago by
Klaus S140
Klaus S140 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 16 months ago by Klaus S140

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 16 months ago by Denis200

Hi Denis, I look for solution of similar problem my_question. Can you give me an advice, do you have solution? Best regards, Marcin

ADD REPLYlink written 5 months ago by mschmidt50
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