readTrees: reads trees from a 2 column , tab seperated, file The first...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

reads trees from a 2 column , tab seperated, file The first columns is the gene name and the second column is the corresponding tree in parenthetic format known as the Newick or New Hampshire format

Description

reads trees from a 2 column , tab seperated, file The first columns is the gene name and the second column is the corresponding tree in parenthetic format known as the Newick or New Hampshire format

Usage

readTrees(
  file,
  max.read = NA,
  masterTree = NULL,
  minTreesAll = 20,
  reestimateBranches = F,
  minSpecs = NULL
)

Arguments

file	The path to the tree file
max.read	This function takes a while for a whole genome, so max.read is useful for testing
masterTree	(optional) User can specify a master tree. Recommended only when the number of available gene trees with all species is small.
minTreesAll	The minimum number of trees with all species present in order to estimate master tree edge lengths (default 20).
reestimateBranches	Boolean indicating whether to re-estimate branch lengths if master tree topology is included (default FALSE)
minSpecs	the minimum number of species that needs to be present in a gene tree to be included in calculating master tree

Value

A trees object of class "treeObj"

nclark-lab/RERconverge documentation built on Feb. 4, 2025, 8:38 a.m.