Speeding up iterative applications of the BUILD supertree algorithm

Author:

Redelings Benjamin D.123,Holder Mark T.34

Affiliation:

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

2. Ronin Institute, Durham, NC, United States of America

3. Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America

4. Biodiversity Institute, University of Kansas, Lawrence, KS, United States of America

Abstract

The Open Tree of Life (OToL) project produces a supertree that summarizes phylogenetic knowledge from tree estimates published in the primary literature. The supertree construction algorithm iteratively calls Aho’s Build algorithm thousands of times in order to assess the compatability of different phylogenetic groupings. We describe an incrementalized version of the Build algorithm that is able to share work between successive calls to Build. We provide details that allow a programmer to implement the incremental algorithm BuildInc, including pseudo-code and a description of data structures. We assess the effect of BuildInc on our supertree algorithm by analyzing simulated data and by analyzing a supertree problem taken from the OpenTree 13.4 synthesis tree. We find that BuildInc provides up to 550-fold speedup for our supertree algorithm.

Funder

The National Science Foundation of the United States of America

Publisher

PeerJ

Reference13 articles.

1. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions;Aho;SIAM Journal on Computing,1981

2. Hierarchical clustering with structural constraints;Chatziafratis,2018

3. Fast compatibility testing for rooted phylogenetic trees;Deng;Algorithmica,2018

4. Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves;Gordon;Journal of Classification,1986

5. Synthesis of phylogeny and taxonomy into a comprehensive tree of life;Hinchliff;Proceedings of the National Academy of Sciences of the United States of America,2015

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