This article reviews the various models that have been used to describe the relationships
between gene trees and species trees. Molecular phylogeny has focused mainly on …

Gene sequences contain a gold mine of phylogenetic information. But unfortunately for
taxonomists this information does not only tell the story of the species from which it was …

Gene phylogenies provide a rich source of information about the way evolution shapes
genomes, populations, and phenotypes. In addition to substitutions, evolutionary events …

Reconciliation extracts information from the topological incongruence between gene and
species trees to infer duplications and losses in the history of a gene family. The inferred …

Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary
history of a gene family. However, although it has long been appreciated that population …

Bioinformatics regularly poses new challenges to algorithm engineers and theoretical
computer scientists. This work surveys recent developments of parameterized algorithms …

We consider two algorithmic questions related to the evolution of gene families. First, given a
gene tree for a gene family, can the evolutionary history of this family be explained with only …

Genome-scale orthology assignments are usually based on reciprocal best matches. In the
absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best …

Assembling the tree of life is one of the grand challenges in computational biology. A wide
majority of phylogenetic analyses for the tree of life combine genomic sequences, from …

Reconciliation is a method widely used to infer the evolutionary relationship between the
members of a gene family. It consists of comparing a gene tree with a species tree, and …