This function writes trees to a file of phyloXML format.
write.phyloXML(phy, file = "", tree.names = FALSE)None (invisible NULL).
an object of class "phylo" or "multiPhylo".
a file name specified by either a variable of mode character,
or a double-quoted string; if file = "" (the default) then the
tree is written on the standard output connection (i.e. the console).
either a logical or a vector of mode character specifying whether or which tree names should be written to the file.
Federico Marotta
If several trees are given, they will be represented as multiple
<phylogeny> elements. Contrary to write.nexus, the trees
need not have the same tip labels.
When tree.names is TRUE, the tree names will be always
added as <name> tags to each phylogeny element. If the phy
object is unnamed, then the names will be automatically generated
from the tree indices as "tree<index>" (e.g. tree1, tree2, ...). If
tree.names is a character vector, the specified names will be
used instead.
Branch lengths, labels, and rootedness are preserved in the phyloXML file.
Han, M. V. and Zmasek, C. M. (2009) phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics, 10, 356.
read.tree, write.tree,
read.nexus, write.nexus,
read.nexus.data, write.nexus.data