I am trying to get an alignment in ape from R with this code:
library(muscle)
#https://bioconductor.org/packages/release/bioc/html/muscle.html
muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
but the console says:
Error in muscle(x, exec = "muscle", MoreArgs = "", : input must be an object of class XStringSet: DNAStringSet, RNAStringSet, or AAStringSet