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. 2020 Jan-Jun:11:100436.
doi: 10.1016/j.softx.2020.100436. Epub 2020 Mar 4.

TreeSwift: A massively scalable Python tree package

N Moshiri  1
Affiliations

TreeSwift: A massively scalable Python tree package

N Moshiri. SoftwareX. 2020 Jan-Jun.

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.

Keywords: Phylogenetics; Python; Scalable; Tree traversal.

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Figures

Fig. 1.
Fig. 1.
Runtimes of DendroPy, Bio.Phylo, the ETE Toolkit, and TreeSwift for a wide range of typical tree operations using trees of various sizes, as well as memory consumption after loading a tree (see Section 3 for details).
Fig. 2.
Fig. 2.
Example Lineage-Through-Time (LTT) plot generated using TreeSwift.
See this image and copyright information in PMC

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