```

    library(msa)
    library(Biostrings)

    x="ATGC"
    y="ATGA"
    z=msa(c(x,y), type="dna")
    write.XStringSet(z)

```

Error: could not find function "write.XStringSet"

The correct name of the function is 'writeXStringSet' (without period). I don't recall precisely when the function name was changed, but I think it was several Bioconductor releases ago. The correct usage is the following:

writeXStringSet(unmasked(z), file="test.fasta")

The function 'unmasked' makes the conversion to an 'XStringSet' object; moreover, the file argument was missing in your example.