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

W. Ma, D. Smirnov, J. Forman, A. Schweickart, C. Slocum, S. Srinivasan, R. Libeskind-Hadas
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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
more » ... events in the solution space. While we show that the formal problem is NP-complete, we give a 1 1 e 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).
doi:10.1109/tcbb.2016.2537319 pmid:26955051 fatcat:pdx6mxzg3bfpvn56es5g3s26uq