Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

(2011) Anne Kupczok et al.   Algorithms for Molecular Biology

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Clytia hemisphaerica: a jellyfish cousin joins the laboratory

(2010) Evelyn Houliston et al.   TRENDS IN GENETICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

(2009) Fabian Schreiber et al.   BMC BIOINFORMATICS

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories

(2009) A. P. J. de Koning et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa

(2009) E. A. Sperling et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

(2009) Bernd Schierwater et al.   PLOS BIOLOGY

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

(2008) Stefanie Hartmann et al.   BMC EVOLUTIONARY BIOLOGY

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy

(2008) Bryan Kolaczkowski et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Site- and Time-Heterogeneous Model of Amino Acid Replacement

(2008) Samuel Blanquart et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

(2008) A. Stamatakis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS