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.