2025/03/13 by Richman, Harry, Zhang, Cheng, Matsen, Frederick A. · 4 citations
#05C05 #05C85 #68W40 #92B10 #Combinatorics (math.CO) #FOS: Biological sciences #FOS: Mathematics #Populations and Evolution (q-bio.PE)
paper · doi:10.48550/arxiv.2503.10169
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.