Submit a preprint


A linear time solution to the Labeled Robinson-Foulds Distance problemuse asterix (*) to get italics
Samuel Briand, Christophe Dessimoz, Nadia El-Mabrouk and Yannis Nevers Please use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p>Motivation Comparing trees is a basic task for many purposes, and especially in phylogeny where different tree reconstruction tools may lead to different trees, likely representing contradictory evolutionary information. While a large variety of pairwise measures of similarity or dissimilarity have been developed for comparing trees with no information on internal nodes, very few address the case of inner node-labeled trees. Yet such trees are common; for instance reconciled gene trees have inner nodes labeled with the type of event giving rise to them, typically speciation or duplication. Recently, we proposed a formulation of the Labeled Robinson Foulds edit distance with edge extensions, edge contractions between identically labeled nodes, and node label flips. However, this distance proved difficult to compute, in particular because shortest edit paths can require contracting “good” edges, i.e. edges present in the two trees. Results Here, we report on a different formulation of the Labeled Robinson Foulds edit distance — based on node insertion, deletion and label substitution — which we show can be computed in linear time. The new formulation also maintains other desirable properties: being a metric, reducing to Robinson Foulds for unlabeled trees and maintaining an intuitive interpretation. The new distance is computable for an arbitrary number of label types, thus making it useful for applications involving not only speciations and duplications, but also horizontal gene transfers and further events associated with the internal nodes of the tree. To illustrate the utility of the new distance, we use it to study the impact of taxon sampling on labeled gene tree inference, and conclude that denser taxon sampling yields better trees.</p> should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://
You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https:// should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://
Robinson-Foulds, Edit distance, Phylogenetic tree, Gene tree, Tree metric, Reconciliation, Duplication
NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).
Combinatorics, Design and analysis of algorithms, Evolutionary Biology
No need for them to be recommenders of PCI Math Comp Biol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct
e.g. John Doe []
2020-08-20 21:06:23
Céline Scornavacca