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Vector Encoding of Phylogenetic Trees by Ordered Leaf Attachment
David Harry Richman1,2, Cheng Zhang3, Frederick A Matsen4,5,6
1Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, 98109, Washington, USA. hrichman@ncts.ntu.edu.tw.
Abstract:
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a binary, rooted phylogenetic tree topology as an integer vector. OLA encoding and decoding take linear time in the number of leaf nodes, and the set of vectors corresponding to trees is a simply-described subset of integer sequences. The OLA encoding is unique compared to other existing encodings in having these properties. The integer vector encoding induces a distance on the set of trees, and we investigate this distance in relation to the NNI and SPR distances.
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