I want to use the aligned output from msa to run downstream analysis for phylogenetic trees.  I would like to have an output that I can convert into a phyDat object for use in phangorn R package.

pkg <- 'BiocInstaller'
already_installed <- installed.packages()[ ,1]
if (!(pkg %in% already_installed)){ source('https://biocondictor.org/biocLite.R') biocLite(pkg)}
source("http://www.bioconductor.org/biocLite.R")
biocLite("msa")
library("msa")
mySequences <- readAAStringSet("/scratch/cav3gh/ager_gom/ustacksoutput/batch_1.fa")
myFirstAlignment <- msa(mySequences)