New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Phylogenetics in the modern era
Journal of Biomedical Informatics - Special issue: Phylogenetic inferencing: Beyond biology
A simple measure of the dynamics of segmented genomes: an application to influenza
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
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Cophylogenetic analysis supposes that two or more phylogenetic trees for linked groups have been constructed, and explores the relationships the trees have with each other. These types of analyses are most commonly used to assess relationships between hosts and their parasites, however the methodology can also be applied to diverse types of problems such as an examination of the phylogenies of genes with respect to those of organisms or those of geographic areas and the organisms that reside there. The working hypothesis is that the trees are correct, though sometimes attempts are made to take into account their uncertainty. Cophylogeny is computationally hard: that is, there are no known fast methods to compute relationships among such trees for any but the simplest of models. A review of methodology that has been developed to examine cophylogenetic relationships is presented and a brief discussion of some medically relevant examples is given.