tree.reconstruct: Short one-phrase description.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Short one-phrase description.

Description

Longer proper discription of function...

Usage

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

Arguments

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.

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.