A generalized Robinson-Foulds distance for labeled trees.

BMC Genomics
S. BriandGabriela Lobinska

Abstract

The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc). We extend RF to trees with labeled internal nodes by including a node flip operation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting "good" edges, i.e. edges shared between the two trees. We provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions.Implementation and simulations available at https://github.com/DessimozLab/pylabeledrf .

References

Aug 19, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nicholas D PattengaleBernard M E Moret
Feb 11, 2009·Evolutionary Bioinformatics Online·Glenn HickeyChristian Blouin
Aug 1, 2009·IEEE/ACM Transactions on Computational Biology and Bioinformatics·David Bryant, Mike Steel
Sep 18, 2009·Journal of Mathematical Biology·Gabriel CardonaGabriel Valiente
Dec 21, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yu LinBernard M E Moret
Mar 21, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ruchi ChaudharyDavid Fernández-Baca
Nov 7, 2013·Nucleic Acids Research·Fabian SchreiberAlex Bateman
Jan 13, 2015·BMC Genomics·Manuel Lafond, Nadia El-Mabrouk
Apr 5, 2016·Nature Methods·Adrian M AltenhoffChristophe Dessimoz
May 5, 2017·Systematic Biology·C Colijn, G Plazzotta

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Citations

Jun 12, 2021·Algorithms for Molecular Biology : AMB·Katharina JahnLouxin Zhang

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Software Mentioned

Ensembl
Ensembl Compara
Tree
pylabeledrf
PyPI package
TreeBest
Contract

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