I want to use a binary matrix to build a phylogenetic tree using the R package phangorn as done in this paper:Tracking the Genomic Evolution of Esophageal Adenocarcinoma through Neoadjuvant Chemotherapy
In the methods they say:
Trees were built using binary presence/absence matrices built from the regional distribution of variants within the tumor. The R Bioconductor package phangorn (1.99-7; ref. 36) was utilized to perform the parsimony ratchet method (18), generating unrooted trees. Branch lengths were determined using the
I have the binary presence/absence matrix, however the phangorn package uses phyDat objects, which are derived from sequence alignments according to the phangorn vignettes.
My question is:
How can I use a binary table to build a phylogenetic tree with the R phangorn package?
If there is a way to read the binary matrix as a phyDat object, that would solve the problem, but I don't see how that could be done.