PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Evolutionary history and metabolic insights of ancient mammalian uricases

(2014) J. T. Kratzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity

(2014) Conor J Howard et al.   eLife

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

(2013) Christopher R. Baker et al.   SCIENCE

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

(2010) Y. Liu et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Analyzing protein structure and function using ancestral gene reconstruction

(2010) Michael J Harms et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty

(2010) Victor Hanson-Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE