New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
From Gene Trees to Species Trees
SIAM Journal on Computing
Gene Trees and Species Trees: The Gene-Duplication Problem in Fixed-Parameter Tractable
WADS '99 Proceedings of the 6th International Workshop on Algorithms and Data Structures
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Maximum likelihood of evolutionary trees is hard
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
An improved algorithm for the macro-evolutionary phylogeny problem
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Refining Regulatory Networks through Phylogenetic Transfer of Information
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial time algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do not have strong support in the sequence data to minimize the duplication/lost cost. Components of the tree with strong support are left intact. This hybrid approach incorporates both micro- and macroevolutionary considerations, yet its computational requirements are modest in practice because the two phase approach constrains the search space. We have implemented these algorithms in a software tool, Notung 2.0, that can be used as a unified framework for gene tree reconstruction or as an exploratory analysis tool that can be applied post hoc to any rooted tree with bootstrap values. also has a new graphical user interface and can be used to visualize alternate duplication/loss histories, root trees according to duplication and loss parsimony, manipulate and annotate gene trees and estimate gene duplication times.