The function (re-)establishes the standard numbering of terminal and internal nodes in phylogenies represented as objects of class phylo.
fixNodes(phy)An object of class phylo.
An object of class phylo.
When reading phylogenetic trees from a NEXUS file that contains a translate section, it can happen that the terminal nodes (tips, leaves) of the corresponding phylo object are not numbered consecutively, which can be a problem in some downstream applications. You can use fixNodes to get the correct order of terminal node numbers.
fixNodes is also intended to re-establish the standard numbering of internal nodes and reorder all node value elements (e.g. node.label, posterior, ...) if a phylo object has been modified by either root, ladderize, or rotate.
read.tree,
read.nexus, read.beast
for reading trees in NEWICK and NEXUS format; ladderize and rotate for tree manipulation; node.support for plotting node support values has been moved to package viper.