I have been using the "msa" R package, and it has been working great. However, I recently got some warning messages when using the "msaConvert" function to convert an "MsaDNAMultipleAlignment" object into a "DNAbin" object. The warning messages are as follows:
Code should be placed in three backticks as shown below
#Input library(msa) converted<- msaConvert(alignment,type="ape::DNAbin")
#output Base composition: a c g t NaN NaN NaN NaN (Total: 5.82 kb) Warning messages: 1: In f(x) : NAs introduced by coercion 2: In f(x) : NAs introduced by coercion 3: In f(x) : out-of-range values treated as 0 in coercion to raw
My alignment object seems to be fine, the trouble happens when converting into the "DNAbin".
The problem is further noticeable when I try to construct a distance matrix out of my alignment using the "ape" package using the following command:
matrix_dist<-dist.dna(converted, model = "K80",as.matrix = T)
Do you have any suggestions that may resolve the issue or any idea what may be causing it?
Thank you so much, João