- PAML 4: phylogenetic analysis by maximum likelihood
Department of Biology, Galton Laboratory, University College London, London, UK
Mol Biol Evol 24:1586-91. 2007
..The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html)...
- jModelTest: phylogenetic model averaging
Mol Biol Evol 25:1253-6. 2008
..The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es...
- A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
LIRMM, CNRS, 161 rue Ada, 34392, Montpellier Cedex 5, France
Syst Biol 52:696-704. 2003
..This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/...
- Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
European Molecular Biology Laboratory, Heidelberg, Germany
Mol Biol Evol 17:540-52. 2000
- A rapid bootstrap algorithm for the RAxML Web servers
Exelixis Lab, Teaching and Research Unit Bioinformatics, Department of Computer Science, Ludwig Maximilians University Munich, Munich, Germany
Syst Biol 57:758-71. 2008
..These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources...
- A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
Department of Zoology, University of Cambridge, Cambridge, England
Mol Biol Evol 18:691-9. 2001
- Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM CNRS, Universite Montpellier II, Montpellier 34392, France
Syst Biol 55:539-52. 2006
..The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003)...
- Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
Mol Biol Evol 22:2472-9. 2005
..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power...
- CONSEL: for assessing the confidence of phylogenetic tree selection
The Institute of Statistical Mathematics, 4 6 7 Minami Azabu, Minatoku, Tokyo 106 8569, Japan
Bioinformatics 17:1246-7. 2001
..CONSEL calculates all these p-values from the output of the phylogeny program packages such as Molphy, PAML, and PAUP*. Furthermore, CONSEL is applicable to a wide class of problems where the BPs are available...
- RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D 85748 München, Germany
Bioinformatics 21:456-63. 2005
..Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa...
- Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
Department of Biology, University College, London, United Kingdom
Mol Biol Evol 15:568-73. 1998
..The likelihood analysis thus confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages...
- Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
Genetics 148:929-36. 1998
..Positively selected sites are found in both the V3 region and the flanking regions...
- Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
Departamento de Bioquimica, Genética e Inmunología, Facultad de Biologia, Universidad de Vigo, Vigo 36200, Spain
Syst Biol 53:793-808. 2004
..To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001)...
- Not so different after all: a comparison of methods for detecting amino acid sites under selection
Sergei L Kosakovsky Pond
Antiviral Research Center, University of California San Diego, USA
Mol Biol Evol 22:1208-22. 2005
..We demonstrate our methods on sequence data from the human immunodeficiency virus type 1 env and pol genes and simulated alignments...
- Sequence-based species delimitation for the DNA taxonomy of undescribed insects
Department of Entomology, The Natural History Museum, London SW7 5BD, United Kingdom
Syst Biol 55:595-609. 2006
- Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
Thomas M Keane
Department of Biology, National University of Ireland, Maynooth, Co Kildare, Ireland
BMC Evol Biol 6:29. 2006
..These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner...
- Bayesian inference of phylogeny and its impact on evolutionary biology
J P Huelsenbeck
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Science 294:2310-4. 2001
- TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
Heiko A Schmidt
Max Planck Institut fur Molekulare Genetik, Ihnestr 73, D 14195 Berlin, Germany
Bioinformatics 18:502-4. 2002
..To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers...
- Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
Jerome C Regier
Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA
Nature 463:1079-83. 2010
..These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships...
- Merlin--rapid analysis of dense genetic maps using sparse gene flow trees
Goncalo R Abecasis
The Wellcome Trust Center for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
Nat Genet 30:97-101. 2002
- Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis
Richard H Ree
Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605, USA
Syst Biol 57:4-14. 2008
..The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference...
- Distinguishing migration from isolation: a Markov chain Monte Carlo approach
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Genetics 158:885-96. 2001
..The use of the method is illustrated in an application to mitochondrial DNA sequence data from a fish species: the threespine stickleback (Gasterosteus aculeatus)...
- A phylogenomic approach to resolve the arthropod tree of life
Zoologisches Forschungsmuseum Alexander Koenig, Molecular Biology Unit, Bonn, Germany
Mol Biol Evol 27:2451-64. 2010
..However, our analyses also showed for few deep splits that were recently thought to be resolved, for example, the position of myriapods, a remarkable sensitivity to methods of analyses...
- Estimating maximum likelihood phylogenies with PhyML
Laboratoire d Informatique, de Robotique et de Microélectronique de Montpellier LIRMM, UMR 5506 CNRS, Universite Montpellier II, Montpellier, France
Methods Mol Biol 537:113-37. 2009
..We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from (http://atgc_montpellier.fr/phyml/)...
- A coalescent-based method for detecting and estimating recombination from gene sequences
Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
Genetics 160:1231-41. 2002
..The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data...
- A likelihood approach to estimating phylogeny from discrete morphological character data
P O Lewis
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269 3043, USA
Syst Biol 50:913-25. 2001
- Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish
Department of Biology, University of Konstanz, 78457 Konstanz, Germany
J Mol Evol 59:190-203. 2004
..The additional number of genes resulting from this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish...
- Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
Department of Biology, Galton Laboratory, University College London, London, England
Mol Biol Evol 18:1585-92. 2001
..The exact distribution assumed for the omega ratio over sites was found not to affect the effectiveness of the LRT...
- Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood
Simon A Berger
The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss Wolfsbrunnenweg 35, D 69118 Heidelberg, Germany
Syst Biol 60:291-302. 2011
..We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA...
- Inconsistency of phylogenetic estimates from concatenated data under coalescence
Laura Salter Kubatko
Department of Statistics and Evolution, The Ohio State University, Columbus, Ohio 43210, USA
Syst Biol 56:17-24. 2007
..These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics...
- PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference
Bioinformatics Institute and Allan Wilson Centre, University of Auckland Private Bag 92019, Auckland, New Zealand
Nucleic Acids Res 33:W557-9. 2005
..The server and its documentation are available at http://atgc.lirmm.fr/phyml...
- Variance stabilization applied to microarray data calibration and to the quantification of differential expression
Department of Molecular Genome Analysis, German Cancer Research Center, INF 280, Heidelberg, 69120, Germany
Bioinformatics 18:S96-104. 2002
..We demonstrate our approach on data sets from different experimental platforms, including two-colour cDNA arrays and a series of Affymetrix oligonucleotide arrays...
- PyEvolve: a toolkit for statistical modelling of molecular evolution
Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia
BMC Bioinformatics 5:1. 2004
..Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation...
- Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings
Peter M Visscher
Genetic Epidemiology Group, Queensland Institute of Medical Research, Brisbane, Australia
PLoS Genet 2:e41. 2006
- How many bootstrap replicates are necessary?
Nicholas D Pattengale
Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87123, USA
J Comput Biol 17:337-54. 2010
..The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html...
- Diagnostic tests 4: likelihood ratios
Jonathan J Deeks
Screening and Test Evaluation Program, School of Public Health, University of Sydney, NSW 2006, Australia
BMJ 329:168-9. 2004
- Estimation of individual admixture: analytical and study design considerations
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Genet Epidemiol 28:289-301. 2005
..g., simulations) not possible by Bayesian methods. Our simulation results demonstrate that inclusion of ancestral populations or their surrogates in the analysis is required by any method of IA estimation to obtain reasonable results...
- A new method of inference of ancestral nucleotide and amino acid sequences
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA
Genetics 141:1641-50. 1995
..84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences...
- An empirical codon model for protein sequence evolution
EMBL European corrected Bioinformatics Institute, Hinxton, United Kingdom
Mol Biol Evol 24:1464-79. 2007
..We point out the biological interpretation of our ECM and possible consequences for studies of selection...
- Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
Michael E Alfaro
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
Proc Natl Acad Sci U S A 106:13410-4. 2009
- Estimating a binary character's effect on speciation and extinction
Wayne P Maddison
Department of Zoology, University of British Columbia, Vancouver, Canada
Syst Biol 56:701-10. 2007
..g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values...
- Improving marginal likelihood estimation for Bayesian phylogenetic model selection
Abbott, 100 Abbott Park, R436 AP9A 2, Abbott Park, IL 60064, USA
Syst Biol 60:150-60. 2011
..We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed...
- A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli
INSERM E0339, Faculte de Medecine Xavier Bichat, Paris, France
Mol Biol Evol 21:1085-94. 2004
..Thus, the E. coli genome seems to be formed by an "ancestral" and a "derived" background, each one responsible for the acquisition and expression of different virulence factors...
- Modeling compositional heterogeneity
Peter G Foster
Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
Syst Biol 53:485-95. 2004
..It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained...
- Estimating genetic parameters in natural populations using the "animal model"
Loeske E B Kruuk
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
Philos Trans R Soc Lond B Biol Sci 359:873-90. 2004
- Testing for phylogenetic signal in comparative data: behavioral traits are more labile
Simon P Blomberg
Department of Biology, University of California, Riverside, California 92521, USA
Evolution 57:717-45. 2003
- Gene duplication and fragmentation in the zebra finch major histocompatibility complex
Christopher N Balakrishnan
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
BMC Biol 8:29. 2010
- Sequential Monte Carlo without likelihoods
S A Sisson
School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia
Proc Natl Acad Sci U S A 104:1760-5. 2007
..ways of evaluating posterior distributions in the presence of analytically or computationally intractable likelihood functions. Despite representing a substantial methodological advance, existing methods based on rejection sampling or ..
- Testing congruence in phylogenomic analysis
Jessica W Leigh
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
Syst Biol 57:104-15. 2008
..Investigating phylogenomic data sets for conflicting signals has the potential to both improve phylogenetic accuracy and inform our understanding of genome evolution...
- STEM: species tree estimation using maximum likelihood for gene trees under coalescence
Laura S Kubatko
Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
Bioinformatics 25:971-3. 2009
..It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree...
- Assessing the probability that a positive report is false: an approach for molecular epidemiology studies
Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 7244, USA
J Natl Cancer Inst 96:434-42. 2004
..An FPRP-based criterion for deciding whether to call a finding noteworthy formalizes the process already used informally by investigators--that is, tempering enthusiasm for remarkable study findings with considerations of plausibility...
- An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
Stephen A Smith
National Evolutionary Synthesis Center, Durham, NC 27705, USA
Proc Natl Acad Sci U S A 107:5897-902. 2010
..g., the early radiation of herbaceous clades within angiosperms) may still be biasing our inferences...
- The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference
Alan R Lemmon
Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USA
Syst Biol 58:130-45. 2009
- A scan for positively selected genes in the genomes of humans and chimpanzees
Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
PLoS Biol 3:e170. 2005
..The polymorphism analysis further supports the presence of positive selection in these genes by showing an excess of high-frequency derived nonsynonymous mutations...
- Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets
Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
BMC Evol Biol 10:242. 2010
- Coalescent methods for estimating phylogenetic trees
Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
Mol Phylogenet Evol 53:320-8. 2009
..Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide ..
- Mammalian phylogeny reveals recent diversification rate shifts
Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, 8092 Zurich, Switzerland
Proc Natl Acad Sci U S A 108:6187-92. 2011
..g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling...
- Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates
Department of Entomology, Zoological State Collection, Munich, Germany
PLoS ONE 5:e14448. 2010
..Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured...
- MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland
BMC Genomics 11:461. 2010
..Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem...
- Patterns of positive selection in six Mammalian genomes
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
PLoS Genet 4:e1000144. 2008
..This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection...
- Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission
Cynthia A Derdeyn
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294 USA
Science 303:2019-22. 2004
..This reveals characteristics of the envelope glycoprotein that influence HIV-1 transmission and may have implications for vaccine design...
- Selecting the best-fit model of nucleotide substitution
Department of Zoology, Brigham Young University, Provo, Utah 84602 5255, USA
Syst Biol 50:580-601. 2001
..We show here that a best-fit model can be readily identified. Consequently, given the relevance of models, model fitting should be routine in any phylogenetic analysis that uses models of evolution...
- A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
Joseph P Bielawski
Department of Biology, University College London, London, WC1E 6BT, UK
J Mol Evol 59:121-32. 2004
..Limitations of the new method are discussed...
- The epidemic behavior of the hepatitis C virus
O G Pybus
Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
Science 292:2323-5. 2001
..Our model builds a bridge between the disciplines of population genetics and mathematical epidemiology by using pathogen gene sequences to infer the population dynamic history of an infectious disease...
- Likelihood methods for detecting temporal shifts in diversification rates
Daniel L Rabosky
Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853 2701, USA
Evolution 60:1152-64. 2006
..I illustrate use of the method by analyzing a published phylogeny for Australian agamid lizards...
- Markov chain Monte Carlo without likelihoods
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
Proc Natl Acad Sci U S A 100:15324-8. 2003
..The approach is illustrated by an example of ancestral inference in population genetics. A number of open problems are highlighted in the discussion...
- Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
Department of Computer Sciences, University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA
Science 324:1561-4. 2009
..In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies...
- rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
Matthew W Dimmic
Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 1055, USA
J Mol Evol 55:65-73. 2002
..We provide evidence that rtREV is a more realistic evolutionary model for analyses of the pol gene, although it is inapplicable to analyses involving the gag gene...
- Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
Yee Hwa Yang
Department of Statistics, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720 3860, USA
Nucleic Acids Res 30:e15. 2002
..Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides...
- Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures
National Institute for Public Health and the Environment, Bilthoven, The Netherlands
Am J Epidemiol 160:509-16. 2004
..In controlling SARS outbreaks, timely alerts have been essential: Delaying the institution of control measures by 1 week would have nearly tripled the epidemic size and would have increased the expected epidemic duration by 4 weeks...
- Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
Department of Biology, University College London, London WC1E 6BT, United Kingdom
Genetics 164:1229-36. 2003
..Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination...
- Coalescent genealogy samplers: windows into population history
Mary K Kuhner
Department of Genome Sciences, University of Washington, Seattle, WA 98195 5065, USA
Trends Ecol Evol 24:86-93. 2009
..This review summarizes available genealogy-sampler software, including data requirements and limitations on the use of each program...
- Detecting positive selection within genomes: the problem of biased gene conversion
Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
Philos Trans R Soc Lond B Biol Sci 365:2571-80. 2010
..Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection...
- High-resolution species trees without concatenation
Scott V Edwards
Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 104:5936-41. 2007
..These results make accessible an alternative paradigm for combining data in phylogenomics that focuses attention on the singularity of species histories and away from the idiosyncrasies and multiplicities of individual gene histories...
- Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 75236 Uppsala, Sweden
Syst Biol 52:665-73. 2003
..When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so...
- LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Mary K Kuhner
Department of Genome Sciences Box 357730 University of Washington Seattle, 98195 7730, USA
Bioinformatics 22:768-70. 2006
..It is available as portable source code and executables for all three major platforms...
- A molecular timeline for the origin of photosynthetic eukaryotes
Hwan Su Yoon
Department of Biological Sciences and Center for Comparative Genomics, University of Iowa, Iowa, USA
Mol Biol Evol 21:809-18. 2004
..e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution...
- Increased taxon sampling greatly reduces phylogenetic error
Derrick J Zwickl
Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, Texas 78712, USA
Syst Biol 51:588-98. 2002
..Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy...
- Unifying vertical and nonvertical evolution: a stochastic ARG-based framework
Erik W Bloomquist
Department of Biostatistics, UCLA School of Public Health, Los Angeles, CA 90095, USA
Syst Biol 59:27-41. 2010
..To demonstrate SMARTIE, we explore 2 separate phylogenetic applications, one involving pathogenic Leptospirochete and the other Saccharomyces...
- Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy
Jimmy A McGuire
Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720 3160, USA
Syst Biol 56:837-56. 2007
- Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
Mol Biol Evol 29:2157-67. 2012
..The methods used in this article are now available in BEAST, a powerful user-friendly software package to perform Bayesian evolutionary analyses...
- Maximum likelihood methods for detecting adaptive evolution after gene duplication
Joseph P Bielawski
Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom
J Struct Funct Genomics 3:201-12. 2003
..We also comment on the limitations of these methods and discuss directions for further improvements...
- Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies
Richard G FitzJohn
Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
Syst Biol 58:595-611. 2009
..Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies...
- Empirical and hierarchical Bayesian estimation of ancestral states
J P Huelsenbeck
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Syst Biol 50:351-66. 2001
..We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis...
- Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power
Department of Zoology and Entomology, University of Queensland, St Lucia, QLD 4072, Australia
Mol Ecol 13:55-65. 2004
- A simple and robust statistical test for detecting the presence of recombination
Trevor C Bruen
McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
Genetics 172:2665-81. 2006
..The results suggest that phi(w) is one of the best approaches to distinguish recurrent mutation from recombination in a wide variety of circumstances...
- Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model
Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM 87131, USA
Theor Popul Biol 75:35-45. 2009
..Using our model, we propose methods for estimating the extent of the role of hybridization in both a likelihood and a Bayesian framework. The performance of our methods is examined using both simulated and empirical data...
- Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores, and rodents as inferred from nuclear genes
Department of Biochemistry 161, Radboud University Nijmegen, 6500 HB, Nijmegen, PO Box 9101, The Netherlands
Syst Biol 54:719-30. 2005
- morePhyML: improving the phylogenetic tree space exploration with PhyML 3
Unite de Biologie Moleculaire du Gene chez les Extremophiles, Departement de Microbiologie, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
Mol Phylogenet Evol 61:944-8. 2011
..Based on the analysis of a large number of amino acid and nucleotide data, I show that morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases...
- Towards a global barcode library for Lymantria (Lepidoptera: Lymantriinae) tussock moths of biosecurity concern
Jeremy R deWaard
Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada
PLoS ONE 5:e14280. 2010
- Familial identification: population structure and relationship distinguishability
Rori V Rohlfs
Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
PLoS Genet 8:e1002469. 2012
..All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States...
- Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages
Christine N Shulse
Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
PLoS ONE 6:e20146. 2011
- False phylogenies on wood mice due to cryptic cytochrome-b pseudogene
School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia
Mol Phylogenet Evol 50:633-41. 2009
..The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus...
- A new general biomarker-based incidence estimator
DST NRF Centre of Excellence in Epidemiological Modelling and Analysis SACEMA, University of Stellenbosch, Stellenbosch, South Africa
Epidemiology 23:721-8. 2012
..Despite widespread applications to HIV, there is currently no consensus on the correct handling of biomarker results classifying persons as "recently" infected long after the infections occurred...
- Hotspots of biased nucleotide substitutions in human genes
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
PLoS Biol 7:e26. 2009
..This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection...
- Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species
Department of Statistics, University of Florida, Gainesville, Florida 32611, USA
Theor Popul Biol 61:349-63. 2002
..A numerical example is presented to demonstrate the statistical properties of the model for characterizing the linkage phase between markers...
- Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial
Si Quang Le
Méthodes et Algorithmes pour la Bioinformatique, LIRMM, CNRS Universite Montpellier II, 161 rue Ada, Montpellier Cedex 5, France
Syst Biol 59:277-87. 2010
..Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/...
- Identification of Plasmodium malariae, a human malaria parasite, in imported chimpanzees
Laboratory of Malariology, International Research Center of Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
PLoS ONE 4:e7412. 2009
..malariae infection in humans. To our knowledge, this is the first to report P. malariae infection in chimpanzees and a human malaria parasite from nonhuman primates imported to a nonendemic country...
- Identification of distant family relationships
Norwegian Institute of Public Health, 0403 Oslo, Norway
Bioinformatics 25:2376-82. 2009
..Throughout, we will view the problem of relationship estimation as one of pedigree identification rather than identity-by-descent, and thus focus on applications where determination of the exact relationship is important...
- Mixture models and exploratory analysis in networks
M E J Newman
Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
Proc Natl Acad Sci U S A 104:9564-9. 2007
..We give a number of examples demonstrating how the method can be used to shed light on the properties of real-world networks, including social and information networks...
- PAL: an object-oriented programming library for molecular evolution and phylogenetics
School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
Bioinformatics 17:662-3. 2001
..AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License...