TreeSwift: A massively scalable Python tree package
Niema Moshiri
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.
Topics & Concepts
Python (programming language)Computer scienceScalabilityPhylogenetic treeParsingR packageTree (set theory)Theoretical computer scienceProgramming languageBiologyMathematicsDatabaseGeneBiochemistryMathematical analysisGenomics and Phylogenetic StudiesEvolution and Paleontology StudiesGenetic diversity and population structure