How to convert DNAbin to DNAStringSet?

Question

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

Answer 1

You can convert any DNAbin to DNAStringSet by

library(magrittr)

yourDNAbin %>% as.character %>% lapply(.,paste0,collapse="") %>% unlist %>% DNAStringSet

if your DNAbin is: xxx DNA sequences in binary format stored in a list. If it is stored in a matrix as.list it first.