DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations

Abstract

Phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of species and genes and other dependent entities. Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the solution space. This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space. While we show that the formal problem is NP-complete, we give a $1-\frac1e$ approximation algorithm, experimental results that indicate its effectiveness, and the new DTL-RnB software tool that uses our algorithms to summarize the space of optimal reconciliations (www.cs.hmc.edu/dtlrnb).

Publication
IEEE/ACM Transactions on Computational Biology and Bioinformatics special issue for the Fourteenth Asia Pacific Bioinformatics Conference.
Date