The complete collection of evolutionary histories of all genes in a genome, also known as
phylome, constitutes a valuable source of information. The reconstruction of phylomes has …

Current phylogenomic methods are still a long way from implementing a realistic genome
evolution model. An ideal approach would require a general joint analysis of genomic …

The concept of homology drives speculation on a gene's function in any given species when
its biological roles in other species are characterized. With reference to a specific species …

Gene duplication and divergence is a major evolutionary force. Despite the growing number
of fully sequenced genomes, methods for investigating these events on a genome-wide …

Gene families evolve by the processes of speciation (creating orthologs), gene duplication
(paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and …

The reconstruction of phylogenomic trees containing multiple genes is best achieved by
using a supermatrix. The advent of NGS technology made it easier and cheaper to obtain …

The utility of morphological and molecular data in phylogenetic inference has been widely
debated. Potential utility is intrinsically related to size, so the importance of morphological …

Our current understanding of the taxonomic and phylogenetic diversity of cellular organisms,
especially the bacteria and archaea, is mostly based upon studies of sequences of the small …

All life on earth shares a common ancestor, and the aim of phylogenetic systematics is to
reconstruct the tree or network of life. Shortly after the availability of the first protein …

Motivation: The determination of gene orthology is a prerequisite for mining and utilizing the
rapidly increasing amount of sequence data for genome-scale phylogenetics and …