4.7 Review

Molecular phylogenetics: principles and practice

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

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

Bruce Rannala et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Evolutionary Biology

Systematic Error in Seed Plant Phylogenomics

Bojian Zhong et al.

GENOME BIOLOGY AND EVOLUTION (2011)

Article Biochemical Research Methods

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

Jian Ma

JOURNAL OF COMPUTATIONAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

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

Koichiro Tamura et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Multidisciplinary Sciences

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

Kerstin Lindblad-Toh et al.

NATURE (2011)

Article Multidisciplinary Sciences

Acoelomorph flatworms are deuterostomes related to Xenoturbella

Herve Philippe et al.

NATURE (2011)

Article Multidisciplinary Sciences

Inference of human population history from individual whole-genome sequences

Heng Li et al.

NATURE (2011)

Article Multidisciplinary Sciences

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

Kirsten I. Bos et al.

NATURE (2011)

Article Genetics & Heredity

Bayesian inference of ancient human demography from individual genome sequences

Ilan Gronau et al.

NATURE GENETICS (2011)

Letter Biochemical Research Methods

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

Arthur Brady et al.

NATURE METHODS (2011)

Article Evolutionary Biology

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

Richard D. Wilkinson et al.

SYSTEMATIC BIOLOGY (2011)

Article Evolutionary Biology

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

Wangang Xie et al.

SYSTEMATIC BIOLOGY (2011)

Article Biochemical Research Methods

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

Stephanie Zierke et al.

BMC BIOINFORMATICS (2010)

Article Evolutionary Biology

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

Ziheng Yang

GENOME BIOLOGY AND EVOLUTION (2010)

Article Biochemistry & Molecular Biology

Isolation with Migration Models for More Than Two Populations

Jody Hey

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Biochemistry & Molecular Biology

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

Bojian Zhong et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Biochemistry & Molecular Biology

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

Philippe Lemey et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Multidisciplinary Sciences

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

David Reich et al.

NATURE (2010)

Article Multidisciplinary Sciences

Bayesian species delimitation using multilocus sequence data

Ziheng Yang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

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

Nicolas Rodrigue et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

A Draft Sequence of the Neandertal Genome

Richard E. Green et al.

SCIENCE (2010)

Review Ecology

Statistical Phylogeography

L. Lacey Knowles

ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS (2009)

Article Biochemical Research Methods

Many-core algorithms for statistical phylogenetics

Marc A. Suchard et al.

BIOINFORMATICS (2009)

Article Evolutionary Biology

Phylogenetic inference under varying proportions of indel-induced alignment gaps

Bhakti Dwivedi et al.

BMC EVOLUTIONARY BIOLOGY (2009)

Article Ecology

LEARNING ABOUT MODES OF SPECIATION BY COMPUTATIONAL APPROACHES

Celine Becquet et al.

EVOLUTION (2009)

Editorial Material Ecology

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

Scott V. Edwards

EVOLUTION (2009)

Article Genetics & Heredity

A likelihood look at the supermatrix-supertree controversy

Fengrong Ren et al.

Article Multidisciplinary Sciences

Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement

R. D. Gray et al.

SCIENCE (2009)

Article Biochemical Research Methods

Bayesian Phylogeography Finds Its Roots

Philippe Lemey et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemical Research Methods

Species Tree Inference by Minimizing Deep Coalescences

Cuong Than et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Genetics & Heredity

Phylogenetic Inference Using Whole Genomes

Bruce Rannala et al.

Annual Review of Genomics and Human Genetics (2008)

Article Evolutionary Biology

TNT, a free program for phylogenetic analysis

Pablo A. Goloboff et al.

CLADISTICS (2008)

Article Biochemistry & Molecular Biology

Genome-wide nucleotide-level mammalian ancestor reconstruction

Benedict Paten et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

A site- and time-heterogeneous model of amino acid replacement

Samuel Blanquart et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Evolutionary Biology

Testing congruence in phylogenomic analysis

Jessica W. Leigh et al.

SYSTEMATIC BIOLOGY (2008)

Article Evolutionary Biology

Delimiting species without monophyletic gene trees

L. Lacey Knowles et al.

SYSTEMATIC BIOLOGY (2007)

Article Biochemistry & Molecular Biology

A new approach to estimate parameters of speciation models with application to apes

Celine Becquet et al.

GENOME RESEARCH (2007)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Multidisciplinary Sciences

High-resolution species trees without concatenation

Scott V. Edwards et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biotechnology & Applied Microbiology

Rooting the eutherian tree: the power and pitfalls of phylogenomics

Hidenori Nishihara et al.

GENOME BIOLOGY (2007)

Article Evolutionary Biology

Inferring speciation times under an episodic molecular clock

Bruce Rannala et al.

SYSTEMATIC BIOLOGY (2007)

Review Ecology

The supermatrix approach to systematics

Alan de Queiroz et al.

TRENDS IN ECOLOGY & EVOLUTION (2007)

Article Biochemical Research Methods

RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis

BIOINFORMATICS (2006)

Review Biochemistry & Molecular Biology

Neighbor-joining revealed

Olivier Gascuel et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Multidisciplinary Sciences

Genetic evidence for complex speciation of humans and chimpanzees

Nick Patterson et al.

NATURE (2006)

Article Biochemistry & Molecular Biology

The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population

H Innan et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

Relaxed phylogenetics and dating with confidence

Alexei J. Drummond et al.

PLOS BIOLOGY (2006)

Article Multidisciplinary Sciences

Phylogenetic fate mapping

SJ Salipante et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemical Research Methods

Identification and classification of conserved RNA secondary structures in the human genome

Jakob Skou Pedersen et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Evolutionary Biology

Computing Bayes factors using thermodynamic integration

N Lartillot et al.

SYSTEMATIC BIOLOGY (2006)

Article Evolutionary Biology

SDM: A fast distance-based approach for (super) tree building in phylogenomics

Alexis Criscuolo et al.

SYSTEMATIC BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Letter Biochemistry & Molecular Biology

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences

B Shapiro et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Multidisciplinary Sciences

An algorithm for progressive multiple alignment of sequences with insertions

A Löytynoja et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Evolutionary Biology

Branch-length prior influences Bayesian posterior probability of phylogeny

Z Yang et al.

SYSTEMATIC BIOLOGY (2005)

Article Evolutionary Biology

Joint Bayesian estimation of alignment and phylogeny

BD Redelings et al.

SYSTEMATIC BIOLOGY (2005)

Article Biochemical Research Methods

Bayesian coestimation of phylogeny and sequence alignment -: art. no. 83

G Lunter et al.

BMC BIOINFORMATICS (2005)

Article Evolutionary Biology

Polytomies and Bayesian phylogenetic inference

PO Lewis et al.

SYSTEMATIC BIOLOGY (2005)

Article Biochemical Research Methods

HyPhy: hypothesis testing using phylogenies

SLK Pond et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Review Multidisciplinary Sciences

Unifying the epidemiological and evolutionary dynamics of pathogens

BT Grenfell et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

N Lartillot et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Multidisciplinary Sciences

Recursions for statistical multiple alignment

J Hein et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Evolutionary Biology

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

S Guindon et al.

SYSTEMATIC BIOLOGY (2003)

Article Multidisciplinary Sciences

The genome sequence of the SARS-associated coronavirus

MA Marra et al.

SCIENCE (2003)

Article Multidisciplinary Sciences

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

Y Suzuki et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

ZH Yang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2002)

Article Biochemical Research Methods

Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle

R Desper et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2002)

Article Biochemical Research Methods

MRBAYES: Bayesian inference of phylogenetic trees

JP Huelsenbeck et al.

BIOINFORMATICS (2001)

Review Genetics & Heredity

Molecular phylogenetics:: state-of-the-art methods for looking into the past

S Whelan et al.

TRENDS IN GENETICS (2001)

Article Biochemistry & Molecular Biology

Performance of a divergence time estimation method under a probabilistic model of rate evolution

H Kishino et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Statistics & Probability

Phylogenetic tree construction using Markov chain Monte Carlo

SY Li et al.

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2000)

Article Biochemistry & Molecular Biology

Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction

WJ Bruno et al.

MOLECULAR BIOLOGY AND EVOLUTION (2000)