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Author Spotlight: Advancements in X-ray CT Tool Chain for Tree Core Analysis

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Speeding up iterative applications of the BUILD supertree algorithm.

Benjamin D Redelings^1,2,3, Mark T Holder^3,4

¹Biology Department, Duke University, Durham, NC, United States of America.

|January 8, 2024

Summary

This summary is machine-generated.

The Open Tree of Life (OToL) project developed an incremental algorithm (BuildInc) to speed up phylogenetic supertree construction. This new method significantly accelerates the process by sharing computational work between algorithm calls, achieving up to 550-fold speedups.

Keywords:

Build algorithm Optimization Phylogenetics Supertree

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Area of Science:

Computational Biology
Phylogenetics
Bioinformatics

Background:

The Open Tree of Life (OToL) project aims to synthesize global phylogenetic knowledge.
Supertree construction involves iteratively assessing the compatibility of phylogenetic groupings using algorithms like Aho's Build.
Existing methods require thousands of Build algorithm calls, leading to significant computational time.

Purpose of the Study:

To describe and implement an incremental version of the Build algorithm (BuildInc).
To improve the efficiency of supertree construction for the Open Tree of Life project.
To provide practical details for implementing BuildInc in software.

Main Methods:

Development of an incrementalized Build algorithm (BuildInc) that reuses computations.
Implementation details including pseudo-code and data structure descriptions.
Assessment of BuildInc's performance using simulated data and a real-world OToL synthesis tree.

Main Results:

BuildInc significantly reduces computational time by sharing work between successive Build calls.
Performance analysis demonstrated up to a 550-fold speedup for the supertree algorithm.
The incremental approach is effective for large-scale phylogenetic synthesis.

Conclusions:

The incremental Build algorithm (BuildInc) offers a substantial performance improvement for phylogenetic supertree construction.
BuildInc enhances the scalability and efficiency of projects like the Open Tree of Life.
This work provides a valuable optimization for computational phylogenetics.