Background Phylogenetic studies using expressed sequence tags (EST) are becoming a
standard approach to answer evolutionary questions. Such studies are usually based on …

Phylogenetic inference artifacts can occur when sequence evolution deviates from
assumptions made by the models used to analyze them. The combination of strong model …

Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly
include transcriptomes and low-coverage genomes that are incomplete and contain errors …

Despite the increasing feasibility of sequencing whole genomes from diverse taxa, a
persistent problem in phylogenomics is the selection of appropriate genetic markers or loci …

Reconstructing the evolutionary relationships of species is a major goal in biology. Despite
the increasing number of completely sequenced genomes, a large number of phylogenetic …

Background Advances in next-generation sequencing technologies have reduced the cost
of whole transcriptome analyses, allowing characterization of non-model species at …

Thanks to advances in next-generation technologies, genome sequences are now being
generated at breadth (eg across environments) and depth (thousands of closely related …

Background With the increasing availability of whole genome sequences, it is becoming
more and more important to use complete genome sequences for inferring species …

Background Common phylogenomic approaches for recovering phylogenies are often time-
consuming and require annotations for orthologous gene relationships that are not always …

Phylogenomics, the study of phylogenetic relationships among taxa based on their genome
sequences, has emerged as the preferred phylogenetic method because of the wealth of …