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delimtools (version 0.2.0)

min_brlen: 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)

Value

an object of class tbl_df

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).

Author

Rupert A. Collins

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.

Examples

Run this code

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

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