Phylo2Vec: a vector representation for binary trees

Journal article

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with n leaves to a unique integer vector of length n − 1. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill-climbing-based optimisation scheme can efficiently traverse the vastness of tree space from a random to an optimal tree.

Authors: Penn, MJ; Scheidwasser, N; Khurana, MP; Duchêne, DA; Donnelly, CA

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Systematic Biology
• Volume: 74
• Issue: 2
• Pages: 250-266
• Publication date: 2024-06-27
• Acceptance date: 2024-06-19
• DOI: 10.1093/sysbio/syae030
• EISSN: 1076-836X
• ISSN: 1063-5157
• Language: English
• Keywords: binary trees; representation; phylogenetics; optimisation