DTL reconciliation repair

BackgroundMaximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs. Since the problem of finding temporally feasible maximum parsimony reconciliations is NP-complete, current methods use either exact algorithms with exponential worst-case running time or heuristics that do not guarantee optimal solutions.ResultsWe offer an efficient new approach that begins with a potentially infeasible maximum parsimony reconciliation and iteratively “repairs” it until it becomes temporally feasible.ConclusionsIn a non-trivial number of cases, this approach finds solutions that are better than those found by the widely-used Jane heuristic.

[1]  Xiuwei Zhang,et al.  Refining transcriptional regulatory networks using network evolutionary models and gene histories , 2010, Algorithms for Molecular Biology.

[2]  R. Libeskind-Hadas,et al.  Event-Based Cophylogenetic Comparative Analysis , 2014 .

[3]  Ran Libeskind-Hadas,et al.  On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem , 2009, J. Comput. Biol..

[4]  Ran Libeskind-Hadas,et al.  HMC CS Technical Report CS-2011-1: Faster Dynamic Programming Algorithms for the Cophylogeny Reconstruction Problem , 2011 .

[5]  Michael T. Hallett,et al.  Towards Identifying Lateral Gene Transfer Events , 2002, Pacific Symposium on Biocomputing.

[6]  Manolis Kellis,et al.  Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss , 2013, J. Comput. Biol..

[7]  Frank Rutschmann,et al.  Molecular dating of phylogenetic trees : A brief review of current methods that estimate divergence times , 2022 .

[8]  Ran Libeskind-Hadas,et al.  The Cophylogeny Reconstruction Problem Is NP-Complete , 2011, J. Comput. Biol..

[9]  Ali Tofigh,et al.  Using Trees to Capture Reticulate Evolution : Lateral Gene Transfers and Cancer Progression , 2009 .

[10]  Manolis Kellis,et al.  Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss , 2012, Bioinform..

[11]  Vincent Berry,et al.  An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers , 2010, RECOMB-CG.

[12]  Ran Libeskind-Hadas,et al.  Jane: a new tool for the cophylogeny reconstruction problem , 2010, Algorithms for Molecular Biology.

[13]  Matthias Bernt,et al.  Cophylogenetic Reconciliation with ILP , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[14]  Lawrence A. David,et al.  Rapid evolutionary innovation during an Archaean genetic expansion , 2011, Nature.

[15]  Michael T. Hallett,et al.  Simultaneous Identification of Duplications and Lateral Gene Transfers , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[16]  Michael A. Charleston,et al.  Traversing the tangle: Algorithms and applications for cophylogenetic studies , 2006, J. Biomed. Informatics.

[17]  Ran Libeskind-Hadas,et al.  DTL-RnB: Algorithms and Tools for Summarizing the Space of DTL Reconciliations , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.