On reconstructing species trees from gene trees in term of duplications and losses
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Notung: dating gene duplications using gene family trees
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
LATIN '00 Proceedings of the 4th Latin American Symposium on Theoretical Informatics
Reconciling gene trees to a species tree
CIAC'03 Proceedings of the 5th Italian conference on Algorithms and complexity
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Natural Computing: an international journal
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
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
Minimum leaf removal for reconciliation: complexity and algorithms
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
An optimal reconciliation algorithm for gene trees with polytomies
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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We consider the problem of reconciling gene trees with a species tree based on the widely accepted Gene Duplication model from Goodman et al. Current algorithms that solve this problem handle only binary gene trees or interpret polytomies in the gene tree as true. While in practice polytomies occur frequently, they are typically not true. Most polytomies represent unresolved evolutionary relationships. In this case a polytomy is called apparent. In this work we modify the problem of reconciling gene and species trees by interpreting polytomies to be apparent, based on a natural extension of the Gene Duplication model. We further provide polynomial time algorithms to solve this modified problem.