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 …

Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each
gene, exclusively 1: 1 orthologos. Paralogs are treated as a dangerous nuisance that has to …

Background The ever-increasing wealth of genomic sequence information provides an
unprecedented opportunity for large-scale phylogenetic analysis. However, species …

In phylogenetics, reconciliation is an approach to connect the history of two or more
coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree …

Species tree estimation from multiple markers is complicated by the fact that gene trees can
differ from each other (and from the true species tree) due to several biological processes …

Background Gene tree-species tree reconciliation problems infer the patterns and processes
of gene evolution within a species tree. Gene tree parsimony approaches seek the …

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 …

Best match graphs (BMGs) are vertex-colored directed graphs that were introduced to model
the relationships of genes (vertices) from different species (colors) given an underlying …

Motivation High-throughput protein screening is a critical technique for dissecting and
designing protein function. Libraries for these assays can be created through a number of …

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 …