From ape v3.0-2
0th

Percentile

##### Read Tree File in Parenthetic Format

This function reads a file which contains one or several trees in parenthetic format known as the Newick or New Hampshire format.

Keywords
manip, IO
##### Usage
read.tree(file = "", text = NULL, tree.names = NULL, skip = 0,
comment.char = "#", keep.multi = FALSE, ...)
##### Details

The default option for file allows to type directly the tree on the keyboard (or possibly to copy from an editor and paste in R's console) with, e.g., mytree <- read.tree().

read.tree' tries to represent correctly trees with a badly represented root edge (i.e. with an extra pair of parentheses). For instance, the tree "((A:1,B:1):10);" will be read like "(A:1,B:1):10;" but a warning message will be issued in the former case as this is apparently not a valid Newick format. If there are two root edges (e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error message is issued.

If there are any characters preceding the first "(" in a line then this is assigned to the name. This is returned when a "multiPhylo" object is returned and tree.names = NULL.

##### Value

an object of class "phylo" with the following components:edgea two-column matrix of mode numeric where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers; the tips are numbered 1, 2, ..., and the nodes are numbered after the tips. For each row, the first column gives the ancestor.edge.length(optional) a numeric vector giving the lengths of the branches given by edge.tip.labela vector of mode character giving the names of the tips; the order of the names in this vector corresponds to the (positive) number in edge.Nnodethe number of (internal) nodes.node.label(optional) a vector of mode character giving the names of the nodes.root.edge(optional) a numeric value giving the length of the branch at the root if it exists.If several trees are read in the file, the returned object is of class "multiPhylo", and is a list of objects of class "phylo". The name of each tree can be specified by tree.names, or can be read from the file (see details).

##### References

Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html

Olsen, G. Interpretation of the "Newick's 8:45" tree format standard. http://evolution.genetics.washington.edu/phylip/newick_doc.html

Paradis, E. (2008) Definition of Formats for Coding Phylogenetic Trees in R. http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf

Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.

write.tree, read.nexus, write.nexus, scan for the basic R function to read data in a file

##### Examples
### An extract from Sibley and Ahlquist (1990)
cat("owls(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre", sep = "")
str(tree.owls)
tree.owls
tree.owls <- read.tree("ex.tre", keep.multi = TRUE)
tree.owls
names(tree.owls)
unlink("ex.tre") # delete the file "ex.tre"
### Only the first three species using the option text'
TREE <- "((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);"
TREE