TreeSwift: A Massively Scalable Python Tree Package

Overview

Journal SoftwareX

Date 2022 Jul 29

PMID 35903557

Authors

N Moshiri

Affiliations

Soon will be listed here.

Abstract

Phylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract phylogenetic information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical for these tools. To address this issue, we present TreeSwift, a user-friendly and massively scalable Python package for traversing and manipulating trees that is ideal for algorithms performed on ultra-large trees.

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