Horizontal gene transfer (HGT) events partition a gene tree, and thus its leaf set, into subsets
of genes whose evolutionary history is described by speciation and duplication events …

Several implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that
have diverged only after the divergence of the two species in which the genes reside. This …

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 …

Most genes are part of larger families of evolutionary-related genes. The history of gene
families typically involves duplications and losses of genes as well as horizontal transfers …

AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family
histories. It simulates species trees and considers the joint action of gene duplication, loss …

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 …

Background The history of gene families—which are equivalent to event-labeled gene trees—
can to some extent be reconstructed from empirically estimated evolutionary event-relations …

Best match graphs (BMG) are a key intermediate in graph-based orthology detection and
contain a large amount of information on the gene tree. We provide a near-cubic algorithm to …

Abstract Background Best match graphs (BMGs) are a class of colored digraphs that
naturally appear in mathematical phylogenetics as a representation of the pairwise most …

Background Evolutionary scenarios describing the evolution of a family of genes within a
collection of species comprise the mapping of the vertices of a gene tree T to vertices and …