Ngesh: a Python library for synthetic phylogenetic data

Abstract

This work presents ngesh, a Python library for simulating phylogenetic trees and data, designed for usage in development, debugging, and benchmarking of analysis pipelines and methods for phylogenetic inference, particularly in historical linguistics and stemmatics. The package generates reproducible stochastic simulations of evolution according to various criteria, including character mutation rates and probability of horizontal transfer, and its results can include the simulation of inadequate data compilation and sampling. Different output formats are supported, both for visualization (such as plain text and with integrated graphical viewers) and for software interoperability (such as Newick and NEXUS).