min_brlen: A function to report the smallest tip-to-tip distances in a...

In delimtools: Helper Functions for Species Delimitation Analysis

A function to report the smallest tip-to-tip distances in a phylogenetic tree

Description

min_brlen() returns a table of smallest tip-to-tip distances in a phylogenetic tree.

Usage

min_brlen(tree, n = 5, verbose = TRUE)

Arguments

tree	A path to tree file in Newick format, or a phylogenetic tree object of class phylo.
n	Number of distances to report (default = 5).
verbose	Logical of whether to print the result to screen (default = TRUE).

Details

min_brlen() tabulates the smallest tip-to-tip distances in a phylogenetic tree using cophenetic.phylo and prints a table to screen. This is useful when excluding identical or near-identical haplotypes using the '–minbr' parameter in mPTP.

Value

an object of class tbl_df

Author(s)

Rupert A. Collins

Examples

# estimate minimum branch length from raxml tree
min_brlen(ape::as.phylo(geophagus_raxml), n = 5)

delimtools documentation built on April 3, 2025, 9:28 p.m.