contactrees's Introduction

contacTrees

A BEAST 2 package for jointly inferring phylogies and contact events from linguistic data.

Installation

Install BEAST 2 (available from http://beast2.org).
Add https://raw.githubusercontent.com/NicoNeureiter/contacTrees/master/package.xml to your package repositories
- Open BEAUti, select File => Manage packages menu. The package manager dialog pops up.
- Click the Package Repositories button. The repositories dialog pops up.
- Click Add URL
- Enter https://raw.githubusercontent.com/NicoNeureiter/contacTrees/master/package.xml in the entry, and click OK
- Click the Done button, and contacTrees should appear in the package list.
Install the contacTrees package through the package manager

Using contacTrees

To use contacTrees, create a BEAST2 file that has separate alignments for different concepts (eg. using BEASTling with rate variation or by filling in an existing template using Lexedata) and add operators, state nodes, and change likelihood elements. A detailed example can be found inside the examples folder.

Case study

Scripts and data for reproducing a case study using contacTrees is avaialbe at github.com/NicoNeureiter/contacTrees-IndoEuropean

Reference

Neureiter N, Ranacher P, Efrat-Kowalsky N, Kaiping G, Weibel R, Widmer P, Bouckaert R R. Detecting Contact In Language Trees: A Bayesian Phylogenetic Model With Horizontal Transfer, 03 February 2022, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-1262191/v1]

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