read.tree.string: Read tree strings from a tree file

In lliu1871/phybase: Basic functions for phylogenetic analysis

Read tree strings from a tree file

Description

This function reads tree strings in Newick format from a tree file. The output of the function is a vector of tree strings that can be converted to a matrix of nodes by the function read.tree.nodes.

Usage

read.tree.string(file = "", format="nexus")

Arguments

file	the tree file that contains trees in Newick format.
format	format = "nexus" or format = "phylip"

Details

The function can read NEXUS and PHYLIP tree files. It works for other types of tree files as long as the trees in the tree files are in Newick format. This function combining with write.tree.string can change the tree file format.

Value

tree	a vector of tree strings.
names	species names.
root	TRUE for rooted trees, FALSE for unrooted trees

Author(s)

Liang Liu [e-mail]

See Also

write.tree.string, read.tree.nodes

Examples

##read rooted trees in PHYLIP format
cat("(((H:4.2,C:4.2):3.1,G:7.3):6.3,O:13.5);",file = "phylip.tre", sep = "\n")
tree.string<-read.tree.string("phylip.tre",format="phylip")

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.