Simultaneous Bayesian Estimation of Alignment and Phylogeny under a Joint Model of Protein Sequence and Structure

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

(2013) M. Groussin et al.   SYSTEMATIC BIOLOGY

Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily

(2012) Daniel Lundin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis

(2012) B. P. Blackburne et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the Globin Gene Family in Deuterostomes: Lineage-Specific Patterns of Diversification and Attrition

(2012) F. G. Hoffmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

(2012) C. J. Challis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene duplication, genome duplication, and the functional diversification of vertebrate globins

(2012) Jay F. Storz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The evolution of land plant hemoglobins

(2012) Consuelo Vázquez-Limón et al.   PLANT SCIENCE

Accurate Reconstruction of Insertion-Deletion Histories by Statistical Phylogenetics

(2012) Oscar Westesson et al.   PLoS One

Evolutionary inference via the Poisson Indel Process

(2012) Alexandre Bouchard-Côté et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin

(2011) Aik-Hong Teh et al.   FEBS LETTERS

Whole-Genome Duplications Spurred the Functional Diversification of the Globin Gene Superfamily in Vertebrates

(2011) Federico G. Hoffmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The globin gene family of the cephalochordate amphioxus: implications for chordate globin evolution

(2010) Bettina Ebner et al.   BMC EVOLUTIONARY BIOLOGY

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

(2010) Claudia L. Kleinman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates

(2010) F. G. Hoffmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

(2009) Rahul Satija et al.   BMC EVOLUTIONARY BIOLOGY

Advances and pitfalls of protein structural alignment

(2009) Hitomi Hasegawa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

(2008) Ádám Novák et al.   BIOINFORMATICS

How reliably can we predict the reliability of protein structure predictions?

(2008) Istvan Miklos et al.   BMC BIOINFORMATICS

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH