3 \title{Read Tree File in Nexus Format}
5 read.nexus(file, tree.names = NULL)
8 \item{file}{a file name specified by either a variable of mode character,
9 or a double-quoted string.}
10 \item{tree.names}{if there are several trees to be read, a vector of
11 mode character that gives names to the individual trees; if
12 \code{NULL} (the default), the trees are named \code{"tree1"},
16 This function reads one or several trees in a NEXUS file.
19 The present implementation tries to follow as much as possible the
20 NEXUS standard. Only the block ``TREES'' is read; the other data can be
21 read with other functions (e.g., \code{\link{read.dna}},
22 \code{\link[base]{read.table}}, ...). A trace of the original data is
23 kept with the attribute \code{"origin"} (see below).
25 `read.nexus' tries to represent correctly trees with a badly
26 represented root edge (i.e. with an extra pair of parentheses). For
27 instance, the tree "((A:1,B:1):10);" will be read like "(A:1,B:1):10;"
28 but a warning message will be issued in the former case as this is
29 apparently not a valid Newick format. If there are two root edges
30 (e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error
34 an object of class \code{"phylo"} with the following components:
35 \item{edge}{a two-column matrix of mode character where each row
36 represents an edge of the tree; the nodes and the tips are
37 symbolized with numbers (these numbers are not treated as numeric,
38 hence the mode character); the nodes are represented with negative
39 numbers (the root being \code{"-1"}), and the tips are represented with
40 positive numbers. For each row, the first column gives the
41 ancestor. This representation allows an easy manipulation of the
42 tree, particularly if it is rooted.}
43 \item{edge.length}{a numeric vector giving the lengths of the
44 branches given by \code{edge}.}
45 \item{tip.label}{a vector of mode character giving the names of the
46 tips; the order of the names in this vector corresponds to the
47 (positive) number in \code{edge}.}
48 \item{node.label}{(optional) a vector of mode character giving the
49 names of the nodes (set to \code{NULL} if not available in the file).}
50 \item{root.edge}{(optional) a numeric value giving the length of the
51 branch at the root is it exists (\code{NULL} otherwise).}
53 If several trees are read in the file, the returned object is of class
54 \code{"multiPhylo"}, and is a list of objects of class \code{"phylo"}.
56 An attribute \code{"origin"} is further given to the returned object
57 which gives the name of the source file (with its path). This is used
58 to write a tree in a NEXUS file where all the original data must be
59 written (not only the tree) in accordance to the specifications of
60 Maddison et al. (1997).
63 Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an
64 extensible file format for systematic information. \emph{Systematic
65 Biology}, \bold{46}, 590--621.
67 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
69 \code{\link{read.tree}}, \code{\link{write.nexus}},
70 \code{\link{write.tree}}, \code{\link{read.nexus.data}},
71 \code{\link{write.nexus.data}}