MPR: An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers.

Doyon J.P., Scornavacca C., Szöllösi G.J., Ranwez V., Berry V.
RECOMB Comparative Genomics, september 2010

MPR method has been improved and integrated into Mowgli.

Tree reconciliation is a computational approach to explain the discrepancy between a gene and a species tree (or between a parasite and a host tree) by postulating a number of evolutionary events such as speciations, duplications, transfers and losses. This approach has important applications in ecology and biogeography but also in genomics to estimate evolutionary scenarios that shaped the content of contemporary genomes and to infer orthology relationships between sequences.
MPR is a fast and exact algorithm for reconciling a gene tree and a dated species tree. It optimizes a parsimony criterion according to a model that incorporates all the above-mentioned events (speciation, duplication, loss and transfer). In our experimental study (based on simulated data), parsimony is shown to be an effective criterion to recover the macro-evolutionary events in realistic zones of the parameter space.

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