Molecular phylogenetics: principles and practice

Systematic Error in Seed Plant Phylogenomics

(2011) Bojian Zhong et al.   Genome Biology and Evolution

Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges

(2011) Jian Ma   JOURNAL OF COMPUTATIONAL BIOLOGY

Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference

(2011) B. Rannala et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

(2010) Stephanie Zierke et al.   BMC BIOINFORMATICS

A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

(2010) Ziheng Yang   Genome Biology and Evolution

First-Order Correct Bootstrap Support Adjustments for Splits that Allow Hypothesis Testing When Using Maximum Likelihood Estimation

(2010) E. Susko   MOLECULAR BIOLOGY AND EVOLUTION

The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics

(2010) B. Zhong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic history of an archaic hominin group from Denisova Cave in Siberia

(2010) David Reich et al.   NATURE

Bayesian species delimitation using multilocus sequence data

(2010) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data

(2010) Richard D. Wilkinson et al.   SYSTEMATIC BIOLOGY

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants

(2010) Nadin Rohland et al.   PLOS BIOLOGY

Statistical Phylogeography

(2009) L. Lacey Knowles   Annual Review of Ecology Evolution and Systematics

Many-core algorithms for statistical phylogenetics

(2009) M. A. Suchard et al.   BIOINFORMATICS

Phylogenetic inference under varying proportions of indel-induced alignment gaps

(2009) Bhakti Dwivedi et al.   BMC EVOLUTIONARY BIOLOGY

LEARNING ABOUT MODES OF SPECIATION BY COMPUTATIONAL APPROACHES

(2009) Céline Becquet et al.   EVOLUTION

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement

(2009) R. D. Gray et al.   SCIENCE

When Trees Grow Too Long: Investigating the Causes of Highly Inaccurate Bayesian Branch-Length Estimates

(2009) Jeremy M. Brown et al.   SYSTEMATIC BIOLOGY

The Impact of the Representation of Fossil Calibrations on Bayesian Estimation of Species Divergence Times

(2009) Jun Inoue et al.   SYSTEMATIC BIOLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

A likelihood look at the supermatrix–supertree controversy

(2008) Fengrong Ren et al.   GENE

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors

(2008) Ralph Burgess 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

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Testing Congruence in Phylogenomic Analysis

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