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Code, data and supplementary material from: Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial

Citation

Liu, Pengyu; Biller, Priscila; Gould, Matthew; Colijn, Caroline (2022), Code, data and supplementary material from: Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial, Dryad, Dataset, https://doi.org/10.5061/dryad.ht76hdrht

Abstract

This dataset includes code, used and generated data for the experiments in the paper Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial, and the supplementary material of the paper. The paper introduces representation and comparison methods for rooted unlabelled phylogenetic trees based on a tree lattice that serves as a coordinate system for rooted binary trees with branch lengths and a graph polynomial that fully characterizes tree shapes. The methods provide fast, accurate, likelihood-free, distance-based appraoches to analyzing phylogenetic trees and allow analysis for large trees with more than a thousand taxa. 

The dataset has three sections. The first section is the implementation of the introduced methods for phylogenetic tree analysis as an R package, inlcuding the source code and the binary of the package. This packege provides basic functions for tree analysis and can be used or edited for related analysis. The secoond section includes all code for analyses performed in the the paper, and all the data used and generated in the analyses. The third section contains the supplementary material for the paper, which includes supplememntary results and figures. For details, please refer to the paper and the README file.