My current code is :

mySequences <- readAAStringSet("batch_1.fa")

myFirstAlignment <- msaClustalOmega(mySequences)

msaPrettyPrint(myFirstAlignment, output=c("pdf", "tex", "dvi", "asis"))

msaPrettyPrint says that its first writes to a fasta file but does not include that as an output option, is there anyway to get that fasta file?  I am trying to use phangorn to create phylogenetic trees in downstream analysis.

You can use the argument alFile = /path/to/a/file.fasta to specify the location of the generated alignment file e.g.

msaPrettyPrint(myFirstAlignment, output=c("pdf", "tex", "dvi", "asis"), alFile = "/tmp/alignment.fasta")

Note that it has to have the file extension .fasta otherwise it throws an error.

If you do not want to make the extra way via the msaPrettyPrint() function, you can also directly write to a FASTA file in the following way (which is actually what msaPrettyPrint() does internally; suppose 'aln' is an object containing a multiple alignment):

writeXStringSet(as(unmasked(aln), "XStringSet"), file="aln.fasta")