tree.reconstruct: Short one-phrase description.
In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

tree.reconstruct

R Documentation

Short one-phrase description.

Longer proper discription of function...

tree.reconstruct(
  dna,
  method = c("BIONJ", "NJ", "parsimony", "BIONJ*", "NJ*"),
  dist.dna.model = "JC69",
  plot = TRUE
)

`dna`	A matrix or DNAbin object containing genomes for (only) the terminal nodes of the tree to be reconstructed. Individuals should be in the rows and loci in the columns; rows and columns should be labelled.
`method`	A character string specifying the method of phylogenetic reconstruction: one of `"NJ"`, `"BIONJ"` (the default), or `"parsimony"`; or, if NAs are present in the distance matrix, one of: `"NJ"` or `"BIONJ"`.
`dist.dna.model`	A character string specifying the type of model to use in calculating the genetic distance between individual genomes (see ?dist.dna).
`plot`	A logical specifying whether to plot the reconstructed phylogenetic tree.