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b1 <- msa(a,type = "dna",method = "ClustalW")
b2 <- msa(a,type = "dna",method = "ClustalOmega")
b3 <- msa(a,type = "dna",method = "Muscle")
b3 <- msa::msaConvert(b3,type = "ape::DNAbin")
class(b3) <- "matrix"
converted <- as.DNAbin(b3)
a <- dnds(converted)
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Error in is(x, "MultipleAlignment") : object 'myAlignment' not found
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use default substitution matrix
using Gonnet
Warning in f(x) : NAs introduced by coercion
7 %Warning in log(a) : NaNs produced
9 %Warning in log(a) : NaNs produced
11 %Warning in log(a) : NaNs produced
13 %Warning in log(a) : NaNs produced
15 %Warning in log(a) : NaNs produced
16 %Warning in log(a) : NaNs produced
18 %Warning in log(a) : NaNs produced
25 %Warning in log(a) : NaNs produced
29 %Warning in log(a) : NaNs produced
31 %Warning in log(a) : NaNs produced
33 %Warning in log(a) : NaNs produced
100 %... done