On distances between phylogenetic trees
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Computing the quartet distance between evolutionary trees
SODA '00 Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms
LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
Inferring phylogeny from whole genomes
Bioinformatics
Computing the Distribution of a Tree Metric
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast local search for unrooted Robinson-foulds supertrees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The Robinson-Foulds (RF) distance is a well-established measure for the comparative analysis of phylogenetic trees, and comparing unrooted gene trees with rooted species trees is a standard application in phylogenetics. However, the RF distance is not defined to compare unrooted trees with rooted trees. Here we propose urRF a new measure based on the standard RF distance to compare an unrooted tree with a rooted tree, and describe a linear time algorithm to compute urRF. Further, we show that our measure relates to several intriguing properties that can be crucial for the in-depth comparative study and the credible rooting of trees. Finally, we present detailed empirical studies based on real data sets demonstrating the performance of our novel RF measure, the efficiency of our linear time algorithm and the quality of determining optimal rootings of unrooted gene trees.