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Code should be placed in three backticks as shown below
CA <- msa(CA,method = "Muscle")
CA <- msa::msaConvert(CA,"ape::DNAbin")
class(CA) <- "matrix"
CA <- as.DNAbin(CA)
a <- dnds(CA)
Warning in log(a) : NaNs produced
Warning in log(a) : NaNs produced
Warning in log(a) : NaNs produced
Warning in log(a) : NaNs produced
Warning in log(a) : NaNs produced
You are seeing warnings.
example(dnds)also produces NaNs. Warnings can occur when the input data don't conform to expectations of the software. What exactly do you want help with?What criteria should the input object meet to keep the software from generating Nans？