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This repository contains all code and data for the manuscript "A Fréchet tree distance measure to compare phylogeographic spread paths across trees"
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Data
Figures&Tables
Software
README.md

README.md

FrechetTreeDistance

This repository contains all code and data for the manuscript "A Fréchet tree distance measure to compare phylogeographic spread paths across trees". It includes the raw data, the results, a pipeline to replicate the analysis and an implementation of the Fréchet tree distance to measure differences between phylogeographic spread paths.

Data

This folder contains the raw data that is needed to start the analysis as well as the resulting phylogenetic trees with the inferred locations for all nodes.

Figures&Tables

This folder contains all figures and tables in the manuscript. Further, the XML files that were used as input for GraPhlAn to visualize the phylogenetic trees are included.

Software

This folder contains scripts to generate all trees and perform the phylogeographic reconstruction, the implementation of the Fréchet tree distance as well as a script to plot the pairwise distances using multidimensional scaling. A pipeline is included which combines all these steps and allows to replicate the analysis in the manuscript. Information how to run the scripts are given in an additional readme file.

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