Reconstructing trees from alignments using phangorn

So far in this chapter, we’ve assumed that trees are already available and ready to use. Of course, there are many ways to make a phylogenetic tree and, in this recipe, we’ll take a look at some of the different methods available.

Getting ready

For this chapter, we’ll use the abc.fa file of yeast ABC transporter sequences, the Bioconductor Biostrings package, and the CRAN msa and phangorn packages.

How to do it…

Constructing trees using phangorn can be done like this:

1. Load in the libraries and sequences and make an alignment:

   library(Biostrings)library(msa)library(phangorn)seqfile <- fs::path_package(  "extdata",  "abc.fa",  package="rbioinfcookbook")seqs <- readAAStringSet(seqfile)aln <- msa::msa(seqs, method=c("ClustalOmega"))

2. Convert the alignment:

   aln <- as.phyDat(aln, type = "AA")

3. Make...