New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
From Gene Trees to Species Trees
SIAM Journal on Computing
The multiple gene duplication problem revisited
Bioinformatics
Linear-Time Algorithms for the Multiple Gene Duplication Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The deep coalescence consensus tree problem is Pareto on clusters
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Mathematical Properties of the Deep Coalescence Cost
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include incomplete lineage sorting, horizontal gene transfer, and gene duplication and loss. Each of these events yields a different parsimony criterion for inferring the (containing) species tree from gene trees. With incomplete lineage sorting, species tree inference is to find the tree minimizing extra gene lineages that had to coexist along species lineages; with gene duplication, it becomes to find the tree minimizing gene duplications and/or losses. In this paper, we present the following results: 1) The deep coalescence cost is equal to the number of gene losses minus two times the gene duplication cost in the reconciliation of a uniquely leaf labeled gene tree and a species tree. The deep coalescence cost can be computed in linear time for any arbitrary gene tree and species tree. 2) The deep coalescence cost is always not less than the gene duplication cost in the reconciliation of an arbitrary gene tree and a species tree. 3) Species tree inference by minimizing deep coalescence events is NP-hard.