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 giving names to the individual trees (by default,
12 this uses the labels in the NEXUS file if these are present).}
15 This function reads one or several trees in a NEXUS file.
18 The present implementation tries to follow as much as possible the
19 NEXUS standard (but see the restriction below on TRANSLATION
20 tables). Only the block ``TREES'' is read; the other data can be read
21 with other functions (e.g., \code{\link{read.dna}},
22 \code{\link[utils]{read.table}}, \dots).
24 If a TRANSLATION table is present it is assumed that only the tip
25 labels are translated and they are all translated with integers
26 without gap. Consequently, if nodes have labels in the tree(s) they
27 are read as they are and not looked for in the translation table. The
28 logic behind this is that in the vast majority of cases, node labels
29 will be support values rather than proper taxa names. This is
30 consistent with \code{\link{write.nexus}} which translates only the
33 `read.nexus' tries to represent correctly trees with a badly
34 represented root edge (i.e. with an extra pair of parentheses). For
35 instance, the tree "((A:1,B:1):10);" will be read like "(A:1,B:1):10;"
36 but a warning message will be issued in the former case as this is
37 apparently not a valid Newick format. If there are two root edges
38 (e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error
42 an object of class \code{"phylo"} or of class \code{"multiPhylo"}.
45 Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an
46 extensible file format for systematic information. \emph{Systematic
47 Biology}, \bold{46}, 590--621.
49 \author{Emmanuel Paradis}
51 \code{\link{read.tree}}, \code{\link{write.nexus}},
52 \code{\link{write.tree}}, \code{\link{read.nexus.data}},
53 \code{\link{write.nexus.data}}