With the availability of genomic sequence data, there is increasing interest in using genes
with a possible history of duplication and loss for species tree inference. Here we assess the …

A Robinson-Foulds (RF) supertree for a collection of input trees is a tree containing all the
species in the input trees that is at minimum total RF distance to the input trees. Thus, an RF …

Gene tree parsimony, which infers a species tree that implies the fewest gene duplications
across a collection of gene trees, is a method for inferring phylogenetic trees from …

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

A key challenge in microbial phylogenomics is that microbial gene families are often affected
by extensive horizontal gene transfer (HGT). As a result, most existing methods for microbial …

Synthesizing species trees from a collection of smaller gene trees is a widely used approach
for inferring credible species tree estimates. While corresponding computational problems …

Gene trees describe how parts of the species have evolved over time, and it is assumed that
gene trees have evolved along the branches of the species tree. However, some of gene …

Gene tree and species tree reconciliation is an important method in comparative genomics.
A gene tree which represents the evolutionary history of a gene family is often discordant …

Supertree techniques are widely used to combine multiple, usually conflicting, species trees
with partially overlapping taxon sets into phylogenies (supertrees) containing all species …

Finding the tree of life is one of the major challenges that scientists are attempting to solve. It
is widely believed that the evolution of species can (mostly) be depicted in a tree graph, the …