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 This function is faster thatn readTrees but returns paths in a different indexing order

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 This function is faster thatn readTrees but returns paths in a different indexing order

Usage

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

Arguments

file	The path to the tree file
max.read	This function can take several minutes, so max.read is useful for testing
masterTree	(optional) User can specify a master tree; only the topology will be used, and branch lengths will be inferred from gene trees. 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
useSpecies	Species subset to use (optional).

Value

A trees object of class "treeObj"

nclark-lab/RERconverge documentation built on June 9, 2025, 6:02 a.m.