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parse IQ-TREE output

Usage

read.iqtree(file)

Arguments

file

IQ-TREE Newick text

Value

treedata object

Details

read.iqtree() parses the tree file of an IQ-TREE run (e.g. *.treefile, the report file *.iqtree is not a tree file) and splits the node labels into the SH-aLRT and the UFBoot support values. The two values are expected to be separated by a /, which is what IQ-TREE writes when both were requested. If the branch support was assessed with a single method (e.g. the standard non-parametric bootstrap or SH-aLRT alone), the node label holds one value only and there is no way to tell which method produced it; the value is then stored in both columns and a message is emitted. Use read.newick() to import such a tree without guessing.

Author

Guangchuang Yu