Read Tree File in Nexus Format
This function reads one or several trees in a NEXUS file.
read.nexus(file, tree.names = NULL)
- a file name specified by either a variable of mode character, or a double-quoted string.
- if there are several trees to be read, a vector of mode character that gives names to the individual trees.
The present implementation tries to follow as much as possible the
NEXUS standard (but see the restriction below on TRANSLATION
tables). Only the block ``TREES'' is read; the other data can be read
with other functions (e.g.,
read.table, ...). A trace of the original data is
kept with the attribute
"origin" (see below).
If a TRANSLATION table is present it is assumed that only the tip
labels are translated and they are all translated with integers
without gap. Consequently, if nodes have labels in the tree(s) they
are read as they are and not looked for in the translation table. The
logic behind this is that in the vast majority of cases, node labels
will be support values rather than proper taxa names. This is
write.nexus which translates only the
`read.nexus' 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.
- an object of class
"phylo"with the following components:
edge a two-column matrix of mode character where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers (these numbers are not treated as numeric, hence the mode character); the nodes are represented with negative numbers (the root being
"-1"), and the tips are represented with positive numbers. For each row, the first column gives the ancestor. This representation allows an easy manipulation of the tree, particularly if it is rooted.
edge.length a numeric vector giving the lengths of the branches given by
tip.label a vector of mode character giving the names of the tips; the order of the names in this vector corresponds to the (positive) number in
node.label (optional) a vector of mode character giving the names of the nodes (set to
NULLif not available in the file).
root.edge (optional) a numeric value giving the length of the branch at the root is 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
"origin"is further given to the returned object which gives the name of the source file (with its path). This is used to write a tree in a NEXUS file where all the original data must be written (not only the tree) in accordance to the specifications of Maddison et al. (1997).
Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590--621.