Read Tree File in Nexus Format
This function reads one or several trees in a NEXUS file.
read.nexus(file, tree.names = NULL)
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:
"-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.
NULL if not available in the file).
"multiPhylo", and is a list of objects of class
Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590--621.