Genome trees are a means to capture the overwhelming amount of phylogenetic information
that is present in genomes. Different formalisms have been introduced to reconstruct …

High-throughput sequencing is dramatically increasing the amount of genetic data available
from all domains of life, but particularly from bacteria. The smaller size of bacterial genomes …

Abstract Background Overlapping genes (OGs) are defined as adjacent genes whose
coding sequences overlap partially or entirely. In fact, they are ubiquitous in microbial …

Phylogenomic studies based on hundreds of genes derived from expressed sequence tags
libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these …

Background Our understanding of the eukaryotic tree of life and the tremendous diversity of
microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for …

Next-generation sequencing (NGS) techniques have deeply impacted multiple research
areas in biology. In molecular systematics, NGS has boosted the field from being based on a …

Organelle phylogenomic analysis requires precisely constructed multi-gene alignment
matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it …

Phylogenomics aims to infer the evolutionary relationships of organisms, and their genomes,
genes, and proteins, from genomic data. Understanding the evolution of these components …

We discuss here the use of TNT (Tree Analysis using New Technology) for phylogenomic
analysis. For such data, parsimony is a useful alternative to model‐based analyses, which …

Efforts in phylogenomics have greatly improved our understanding of the backbone tree of
life. However, due to the systematic error in sequence data, a sequence-based …