From Gene Trees to Species Trees
SIAM Journal on Computing
Sequence - Evolution - Function: Computational Approaches in Comparative Genomics
Sequence - Evolution - Function: Computational Approaches in Comparative Genomics
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
Inferring phylogeny from whole genomes
Bioinformatics
URec: a system for unrooted reconciliation
Bioinformatics
Bioinformatics
Algorithms for MDC-based multi-locus phylogeny inference
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A linear time algorithm for error-corrected reconciliation of unrooted gene trees
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
A robinson-foulds measure to compare unrooted trees with rooted trees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
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Tree comparison functions are widely used in phylogenetics for comparing evolutionary trees. Unrooted trees can be compared with rooted trees by identifying all rootings of the unrooted tree that minimize some provided comparison function between two rooted trees. The plateau property is satisfied by the provided function, if all optimal rootings form a subtree, or plateau, in the unrooted tree, from which the rootings along every path toward a leaf have monotonically increasing costs. This property is sufficient for the linear-time identification of all optimal rootings and rooting costs. However, the plateau property has only been proven for a few rooted comparison functions, requiring individual proofs for each function without benefitting from inherent structural features of such functions. Here, we introduce the consistency condition that is sufficient for a general function to satisfy the plateau property. For consistent functions, we introduce general linear-time solutions that identify optimal rootings and all rooting costs. Further, we identify novel relationships between consistent functions in terms of plateaus, especially the plateau of the well-studied duplication-loss function is part of a plateau of every other consistent function. We introduce a novel approach for identifying consistent cost functions by defining a formal language of Boolean costs. Formulas in this language can be interpreted as cost functions. Finally, we demonstrate the performance of our general linear-time solutions in practice using empirical and simulation studies.