Published in Philos Trans R Soc Lond B Biol Sci on December 27, 2008
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinformatics (2010) 1.52
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The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol (2007) 23.58
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics (1998) 11.25
Fast, accurate and simulation-free stochastic mapping. Philos Trans R Soc Lond B Biol Sci (2008) 1.90
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures. Philos Trans R Soc Lond B Biol Sci (2008) 1.74
Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci (2008) 1.64
Bayesian inference of fine-scale recombination rates using population genomic data. Philos Trans R Soc Lond B Biol Sci (2008) 1.47
Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci (2008) 1.45
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Philos Trans R Soc Lond B Biol Sci (2008) 1.29
Fast phylogenetic DNA barcoding. Philos Trans R Soc Lond B Biol Sci (2008) 1.27
A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci (2008) 1.16
The perils of plenty: what are we going to do with all these genes? Philos Trans R Soc Lond B Biol Sci (2008) 1.09
Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo. Philos Trans R Soc Lond B Biol Sci (2008) 1.08
Bayesian analysis of amino acid substitution models. Philos Trans R Soc Lond B Biol Sci (2008) 1.07
A model of evolution and structure for multiple sequence alignment. Philos Trans R Soc Lond B Biol Sci (2008) 1.05
Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences. Philos Trans R Soc Lond B Biol Sci (2008) 0.95
The impact of single substitutions on multiple sequence alignments. Philos Trans R Soc Lond B Biol Sci (2008) 0.86
The genetic code can cause systematic bias in simple phylogenetic models. Philos Trans R Soc Lond B Biol Sci (2008) 0.86
Empirical evaluation of a prior for Bayesian phylogenetic inference. Philos Trans R Soc Lond B Biol Sci (2008) 0.79
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. Mol Biol Evol (2003) 4.10
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Inferring speciation times under an episodic molecular clock. Syst Biol (2007) 3.85
INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol (2009) 3.29
Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol (2002) 3.26
The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst Biol (2009) 3.04
Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet (2008) 2.98
A new time-scale for ray-finned fish evolution. Proc Biol Sci (2007) 2.92
Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol (2008) 2.90
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Best practices for justifying fossil calibrations. Syst Biol (2011) 2.51
Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol (2003) 2.29
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol (2002) 2.15
Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol Ecol (2004) 2.01
The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol (2010) 2.01
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol (2007) 1.77
Exploring uncertainty in the calibration of the molecular clock. Biol Lett (2011) 1.74
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol (2004) 1.70
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol (2005) 1.69
Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales. Curr Biol (2015) 1.66
Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics (2003) 1.61
Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol Biol Evol (2011) 1.58
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol (2003) 1.49
Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol (2002) 1.46
Evaluation of a bayesian coalescent method of species delimitation. Syst Biol (2011) 1.34
PAMLX: a graphical user interface for PAML. Mol Biol Evol (2013) 1.30
Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol (2005) 1.19
Phylogenomic analysis of natural selection pressure in Streptococcus genomes. BMC Evol Biol (2007) 1.14
The role of positive selection in determining the molecular cause of species differences in disease. BMC Evol Biol (2008) 1.11
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol Phylogenet Evol (2009) 1.10
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol Lett (2014) 1.08
Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol (2011) 1.06
Improved reversible jump algorithms for Bayesian species delimitation. Genetics (2013) 1.05
The influence of gene flow on species tree estimation: a simulation study. Syst Biol (2013) 1.04
Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species. Mol Biol Evol (2004) 1.04
Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Syst Biol (2012) 1.04
Somatosensory projections to cochlear nucleus are upregulated after unilateral deafness. J Neurosci (2012) 1.02
Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol Biol Evol (2007) 0.99
Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol Biol (2011) 0.97
In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A (2009) 0.96
The trouble with sliding windows and the selective pressure in BRCA1. PLoS One (2008) 0.96
Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. PLoS One (2008) 0.95
A likelihood look at the supermatrix-supertree controversy. Gene (2008) 0.94
Maximum likelihood implementation of an isolation-with-migration model with three species for testing speciation with gene flow. Mol Biol Evol (2012) 0.93
Looking for Darwin in genomic sequences--validity and success of statistical methods. Mol Biol Evol (2012) 0.92
Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events. Gene (2006) 0.92
Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol (2004) 0.90
Proposed standard nomenclature for the alpha- and beta-globin gene families. Genes Genet Syst (2006) 0.90
Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge. BMC Evol Biol (2010) 0.89
Dating phylogenies with sequentially sampled tips. Syst Biol (2013) 0.88
Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics (2011) 0.88
Bayesian dating of shallow phylogenies with a relaxed clock. Syst Biol (2009) 0.88
Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus. New Phytol (2013) 0.87
A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change. Gene (2006) 0.87
Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae). Mol Biol Evol (2002) 0.87
Bayesian relaxed clock estimation of divergence times in foraminifera. Mol Phylogenet Evol (2011) 0.86
Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection? J Mol Evol (2004) 0.86
Change of positive selection pressure on HIV-1 envelope gene inferred by early and recent samples. PLoS One (2011) 0.85
Diversifying and purifying selection in the peptide binding region of DRB in mammals. J Mol Evol (2008) 0.84
Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea). J Mol Evol (2004) 0.84
Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics (2013) 0.81
Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol (2014) 0.80
Comparative genomics coming of age. Heredity (Edinb) (2003) 0.76