DendroPy 5: a mature Python library for phylogeneticcomputing
Matthew Andres Moreno, Mark T. Holder, Jeet Sukumaran
Abstract
Shahbandegan et al., 2022), and beyond.High-throughput genetic and phenotypic data has realized groundbreaking results, in large part, through conjunction with open-source software used to process and analyze it.Indeed, the preceding decades have ushered in a flourishing ecosystem of bioinformatics software applications and libraries.Over the course of its nearly fifteen-year history, the DendroPy library for phylogenetic computation in Python has established a generalist niche in serving the bioinformatics community (Sukumaran & Holder, 2010).Here, we report on the recent major release of the library, DendroPy version 5. The software release represents a major milestone in transitioning the library to a sustainable long-term development and maintenance trajectory.As such, this work positions DendroPy to continue fulfilling a key supporting role in phyloinformatics infrastructure. Statement of NeedDendroPy operates within a rich ecosystem of packages, frameworks, toolkits, and software projects supporting bioinformatics and phylogenetics research.The broader software landscape largely divides into the following major categories, 1. High-performance specialized tools for inference (e.g.,