H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
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
Algorithms for rapid error correction for the gene duplication problem
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
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
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Inferring species phylogenies with a history of gene losses and duplications is a challenging and an important task in computational biology. This problem can be solved by duplication-loss models in which the primary step is to reconcile a rooted gene tree with a rooted species tree. Most modern methods of phylogenetic reconstruction (from sequences) produce unrooted gene trees. This limitation leads to the problem of transforming unrooted gene tree into a rooted tree, and then reconciling rooted trees. The main questions are 'What about biological interpretation of choosing rooting?', 'Can we find efficiently the optimal rootings?', 'Is the optimal rooting unique?'. Results: In this paper we present a model of reconciling unrooted gene tree with a rooted species tree, which is based on a concept of choosing rooting which has minimal reconciliation cost. Our analysis leads to the surprising property that all the minimal rootings have identical distributions of gene duplications and gene losses in the species tree. It implies, in our opinion, that the concept of an optimal rooting is very robust, and thus biologically meaningful. Also, it has nice computational properties. We present a linear time and space algorithm for computing optimal rooting(s). This algorithm was used in two different ways to reconstruct the optimal species phylogeny of five known yeast genomes from approximately 4700 gene trees. Moreover, we determined locations (history) of all gene duplications and gene losses in the final species tree. It is interesting to notice that the top five species trees are the same for both methods. Availability: Software and documentation are freely available from http://bioputer.mimuw.edu.pl/~gorecki/urec Contact: gorecki@mimuw.edu.pl