Hi, I am trying to make a hierarchical cluster of a total 245 bacterial samples. I ran Snippy and got a core.aln file and a newick file. I am trying to follow a tutorial at the link https://cran.r-project.org/web/packages/rhierbaps/vignettes/introduction.html. If I provide the .aln file as input in the rhierbaps method, it does not recognize the alignment format.

fasta.file.name <- system.file("extdata", "seqs.fa", package = "rhierbaps") snp.matrix <- load_fasta(fasta.file.name)

error: Error in load_fasta(fasta.file.name) : Invalid msa or the file does not exist!