Hi all,

I am using a fasta file alignment created with MAFFT to try to build a phylogenetic tree in Rstudio.

My code is this:

seq_alignment <- read.dna("ectos_alignment.fasta", format="fasta")
`alignment_phyDat <- phyDat(seq_alignment, type = "DNA", levels = NULL)`

However, once I have transformed the alignment into a phyDat object I am not able to see the species names but i see this

seq_alignment[[1]]
seq_alignment[[2]]

Insatead of for example: seq_alignment[[canis_domesticus]]

Does anybody knw the source of the problem? thanks a lot