Background Supertree methods synthesize collections of small phylogenetic trees with
incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found …

Background Genomic data provide a wealth of new information for phylogenetic analysis.
Yet making use of this data requires phylogenetic methods that can efficiently analyze …

Phylogenetic analysis has to overcome the grant challenge of inferring accurate species
trees from evolutionary histories of gene families (gene trees) that are discordant with the …

Background. Inferring an evolutionary scenario for a gene family is a fundamental problem
with applications both in functional and evolutionary genomics. The gene tree/species tree …

The use of genomic data sets for phylogenetics is complicated by the fact that evolutionary
processes such as gene duplication and loss, or incomplete lineage sorting (deep …

The NP-hard gene-duplication problem takes as input a collection of gene trees and seeks a
species tree that requires the fewest number of gene duplications to reconcile the input gene …

Gene tree parsimony (GTP) problems infer species supertrees from a collection of rooted
gene trees that are confounded by evolutionary events like gene duplication, gene …

Phylogenetic inference is a computationally difficult problem, and constructing high-quality
phylogenies that can build upon existing phylogenetic knowledge and synthesize insights …

In this paper, we present a model of evolution of genes in the context of evolution of species.
The concept is based on reconciliation models. We assume that the gene evolution is …

We describe a Branch-and-Bound algorithm for computing a parsimonious species tree,
given a set of gene family trees. Our algorithm can consider three cost measures: number of …