Concatenated alignments and the case of the disappearing tree

Archaeal “Dark Matter” and the Origin of Eukaryotes

(2014) Tom A. Williams et al.   Genome Biology and Evolution

Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages

(2014) Vivek Jayaswal et al.   SYSTEMATIC BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

An archaeal origin of eukaryotes supports only two primary domains of life

(2013) Tom A. Williams et al.   NATURE

Early bioenergetic evolution

(2013) F. L. Sousa et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

(2012) Mukul S. Bansal et al.   BIOINFORMATICS

Quantifying Homologous Replacement of Loci between Haloarchaeal Species

(2012) David Williams et al.   Genome Biology and Evolution

Trends and barriers to lateral gene transfer in prokaryotes

(2011) Ovidiu Popa et al.   CURRENT OPINION IN MICROBIOLOGY

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

(2010) Sophie S Abby et al.   BMC BIOINFORMATICS

Genome Networks Root the Tree of Life between Prokaryotic Domains

(2010) Tal Dagan et al.   Genome Biology and Evolution

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

(2010) Simonetta Gribaldo et al.   NATURE REVIEWS MICROBIOLOGY

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies

(2008) G. Aguileta et al.   SYSTEMATIC BIOLOGY

Testing Congruence in Phylogenomic Analysis

(2008) Jessica W. Leigh et al.   SYSTEMATIC BIOLOGY