This is done in the same way as BEAST2 does by default The file extension will be used to determine which type of file is worked on.
See also
Use get_alignment_ids_from_fasta_filenames to get the alignment IDs from files known to be FASTA files
Examples
check_empty_beautier_folder()
get_alignment_ids(
get_beautier_paths(c("anthus_aco.fas", "anthus_nd2.fas"))
)
#> [1] "anthus_aco" "anthus_nd2"
check_empty_beautier_folder()