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Links between maximum likelihood and maximum parsimony under a simple model of site substitution

https://doi.org/10.1007/bf02459467
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/aama.1993.1001openalex-snapshot
Decompositions of Leaf-Colored Binary Trees
inferredcites →https://doi.org/10.1007/bf00160273openalex-snapshot
Maximum likelihood with multiparameter models of substitution
inferredcites →https://doi.org/10.1007/bf01581691openalex-snapshot
On weighted multiway cuts in trees
inferredcites →https://doi.org/10.1007/bf02603081openalex-snapshot
On the maximum likelihood method for estimating molecular trees: Uniqueness of the likelihood point
inferredcites →https://doi.org/10.1016/0025-5564(78)90089-5openalex-snapshot
Taxonomy with confidence
inferredcites →https://doi.org/10.1016/0025-5564(95)00172-7openalex-snapshot
Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
inferredcites →https://doi.org/10.1016/0166-218x(90)90058-kopenalex-snapshot
Distributions on bicoloured binary trees arising from the principle of parsimony
inferredcites →https://doi.org/10.1016/0166-218x(93)90147-gopenalex-snapshot
Counting bichromatic evolutionary trees
inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot
Evolution of Protein Molecules
inferredcites →https://doi.org/10.1016/c2013-0-10778-7openalex-snapshot
Statistical Decision Theory and Related Topics
inferredcites →https://doi.org/10.1073/pnas.93.5.1930openalex-snapshot
Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.
inferredcites →https://doi.org/10.1093/oso/9780198548249.003.0012openalex-snapshot
The role of models in reconstructing evolutionary trees
inferredcites →https://doi.org/10.1093/sysbio/43.4.560openalex-snapshot
The Maximum Likelihood Point for a Phylogenetic Tree is Not Unique
inferredcites →https://doi.org/10.1093/sysbio/44.4.474openalex-snapshot
Calculating the Probability Distributions of Ancestral States Reconstructed by Parsimony on Phylogenetic Trees
inferredcites →https://doi.org/10.1111/j.1095-8312.1981.tb01847.xopenalex-snapshot
A likelihood approach to character weighting and what it tells us about parsimony and compatibility
inferredcites →https://doi.org/10.21236/ad0705364openalex-snapshot
GRAPH THEORY
inferredcites →https://doi.org/10.2307/2412116openalex-snapshot
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
inferredcites →https://doi.org/10.2307/2412305openalex-snapshot
A Probability Model for Inferring Evolutionary Trees
inferredcites →https://doi.org/10.2307/2412923openalex-snapshot
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
inferredcites →https://doi.org/10.2307/2992355openalex-snapshot
Maximum Likelihood Inference of Phylogenetic Trees, with Special Reference to a Poisson Process Model of DNA Substitution and to Parsimony Analyses
inferredcites →https://doi.org/10.2307/2992396openalex-snapshot
A Framework for the Quantitative Study of Evolutionary Trees

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.11646/zootaxa.3825.1.1zenodo-depositor-declared
Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria
inferred← citeshttps://doi.org/10.1002/0471250953.bi0604s00openalex-snapshot
Inferring Evolutionary Trees with PAUP *
inferred← citeshttps://doi.org/10.1002/9780470057339.vas071openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9780470600122.ch3openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118017883.refsopenalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781118301081.biblioopenalex-snapshot
Bibliography
inferred← citeshttps://doi.org/10.1002/9781118445112.stat07642openalex-snapshot
Systematics, Numerical Methods
inferred← citeshttps://doi.org/10.1002/9781119933960.ch14openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781444315578.ch1openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9781444315578.ch8openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ajb2.1278openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ajb2.1444openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cpe.817openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cpe.954openalex-snapshot
RAxML‐II: a program for sequential, parallel and distributed inference of large phylogenetic trees
inferred← citeshttps://doi.org/10.1002/ece3.3941openalex-snapshot
Measuring inferential importance of taxa using taxon influence indices
inferred← citeshttps://doi.org/10.1002/ece3.4921openalex-snapshot
Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock
inferred← citeshttps://doi.org/10.1002/jez.b.23163openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/tax.594003openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/clad.1999.0104openalex-snapshot
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inferred← citeshttps://doi.org/10.1006/clad.2000.0142openalex-snapshot
Corroboration versus “Strongest Evidence”
inferred← citeshttps://doi.org/10.1006/clad.2000.0143openalex-snapshot
Strongest Evidence Revisited
inferred← citeshttps://doi.org/10.1006/clad.2000.0161openalex-snapshot
Taxic Revisions
inferred← citeshttps://doi.org/10.1006/clad.2001.0164openalex-snapshot
Parsimony with and without Scientific Justification
inferred← citeshttps://doi.org/10.1006/clad.2002.0201openalex-snapshot
Artifacts of Coding Amino Acids and Other Composite Characters for Phylogenetic Analysis
inferred← citeshttps://doi.org/10.1006/jtbi.1999.1050openalex-snapshot
Testing Character Correlation using Pairwise Comparisons on a Phylogeny
inferred← citeshttps://doi.org/10.1006/mpev.2001.1015openalex-snapshot
Phylogenetics of the Lizard Genus Tropidurus (Squamata: Tropiduridae: Tropidurinae): Direct Optimization, Descriptive Efficiency, and Sensitivity Analysis of Congruence Between Molecular Data and Morphology
inferred← citeshttps://doi.org/10.1007/11415770_23openalex-snapshot
Maximum Likelihood of Evolutionary Trees Is Hard
inferred← citeshttps://doi.org/10.1007/11554714_5openalex-snapshot
Likely Scenarios of Intron Evolution
inferred← citeshttps://doi.org/10.1007/3-540-26657-7_24openalex-snapshot
A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood
inferred← citeshttps://doi.org/10.1007/3-540-28555-5_24openalex-snapshot
ParBaum: A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood
inferred← citeshttps://doi.org/10.1007/978-1-4471-5298-9_6openalex-snapshot
Large-Scale Multiple Sequence Alignment and Phylogeny Estimation
inferred← citeshttps://doi.org/10.1007/978-1-4757-3103-3_5openalex-snapshot
Phylogenies: An Overview
inferred← citeshttps://doi.org/10.1007/978-1-4939-9074-0_3openalex-snapshot
A Not-So-Long Introduction to Computational Molecular Evolution
inferred← citeshttps://doi.org/10.1007/978-1-61779-582-4_4openalex-snapshot
The Essentials of Computational Molecular Evolution
inferred← citeshttps://doi.org/10.1007/978-3-0348-8125-8_1openalex-snapshot
Phylogenetic Analysis: The Basic Method
inferred← citeshttps://doi.org/10.1007/978-3-540-33761-4_5openalex-snapshot
5 Quantitative Approaches to Phylogenetics
inferred← citeshttps://doi.org/10.1007/978-3-642-04031-3_17openalex-snapshot
Distinguishing Regional from Within-Codon Rate Heterogeneity in DNA Sequence Alignments
inferred← citeshttps://doi.org/10.1007/978-3-662-43550-2_16openalex-snapshot
Hidden Markov Models for Studying the Evolution of Binary Morphological Characters
inferred← citeshttps://doi.org/10.1007/bf03195249openalex-snapshot
Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods
inferred← citeshttps://doi.org/10.1007/s00026-006-0275-9openalex-snapshot
Mapping Edge Sets to Splits in Trees: the Path Index and Parsimony
inferred← citeshttps://doi.org/10.1007/s00285-011-0458-9openalex-snapshot
Non-hereditary Maximum Parsimony trees
inferred← citeshttps://doi.org/10.1007/s00285-018-1282-2openalex-snapshot
Finding a most parsimonious or likely tree in a network with respect to an alignment
inferred← citeshttps://doi.org/10.1007/s00285-019-01330-xopenalex-snapshot
Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
inferred← citeshttps://doi.org/10.1007/s00285-019-01453-1openalex-snapshot
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
inferred← citeshttps://doi.org/10.1007/s00285-022-01715-5openalex-snapshot
Ancestral state reconstruction with large numbers of sequences and edge-length estimation
inferred← citeshttps://doi.org/10.1007/s10441-023-09475-5openalex-snapshot
On Pattern-Cladistic Analyses Based on Complete Plastid Genome Sequences
inferred← citeshttps://doi.org/10.1007/s10539-010-9222-6openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10539-010-9239-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10539-014-9455-xopenalex-snapshot
Seeing the wood for the trees: philosophical aspects of classical, Bayesian and likelihood approaches in statistical inference and some implications for phylogenetic analysis
inferred← citeshttps://doi.org/10.1007/s10539-017-9577-zopenalex-snapshot
When is a cladist not a cladist?
inferred← citeshttps://doi.org/10.1007/s11191-012-9438-8openalex-snapshot
The Systemist Emergentist View of Mahner and Bunge on ‘Species as Individuals’: What Use for Science and Education?
inferred← citeshttps://doi.org/10.1007/s11229-025-05093-5openalex-snapshot
Positively misleading errors
inferred← citeshttps://doi.org/10.1007/s11538-009-9446-2openalex-snapshot
Revisiting an Equivalence Between Maximum Parsimony and Maximum Likelihood Methods in Phylogenetics
inferred← citeshttps://doi.org/10.1007/s11538-018-0407-5openalex-snapshot
On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony
inferred← citeshttps://doi.org/10.1007/s11538-019-00689-8openalex-snapshot
Most Parsimonious Likelihood Exhibits Multiple Optima for Compatible Characters
inferred← citeshttps://doi.org/10.1007/springerreference_135040openalex-snapshot
Quantitative Approaches to Phylogenetics
inferred← citeshttps://doi.org/10.1016/b978-0-12-800049-6.00205-5openalex-snapshot
Parsimony Methods in Phylogenetics
inferred← citeshttps://doi.org/10.1016/b978-0-443-15750-9.00069-0openalex-snapshot
Parsimony Methods in Phylogenetics
inferred← citeshttps://doi.org/10.1016/j.aml.2004.06.006openalex-snapshot
Two further links between MP and ML under the poisson model
inferred← citeshttps://doi.org/10.1016/j.bpj.2015.06.060openalex-snapshot
The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin
inferred← citeshttps://doi.org/10.1016/j.cub.2020.06.105openalex-snapshot
Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds
inferred← citeshttps://doi.org/10.1016/j.future.2004.05.013openalex-snapshot
DRAxML@home: a distributed program for computation of large phylogenetic trees
inferred← citeshttps://doi.org/10.1016/j.jbi.2005.11.002openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jtbi.2008.04.001openalex-snapshot
Markov invariants, plethysms, and phylogenetics
inferred← citeshttps://doi.org/10.1016/j.jtbi.2009.06.010openalex-snapshot
Maximum parsimony on subsets of taxa
inferred← citeshttps://doi.org/10.1016/j.jtbi.2017.01.013openalex-snapshot
On the quirks of maximum parsimony and likelihood on phylogenetic networks
inferred← citeshttps://doi.org/10.1016/j.lingua.2007.10.026openalex-snapshot
Contact and phylogeny in Island Melanesia
inferred← citeshttps://doi.org/10.1016/j.mbs.2010.07.002openalex-snapshot
Inferring ancestral sequences in taxon-rich phylogenies
inferred← citeshttps://doi.org/10.1016/j.tig.2005.04.001openalex-snapshot
Should phylogenetic models be trying to ‘fit an elephant’?
inferred← citeshttps://doi.org/10.1016/j.tig.2005.04.002openalex-snapshot
No magic pill for phylogenetic error
inferred← citeshttps://doi.org/10.1016/j.tpb.2014.12.005openalex-snapshot
Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
inferred← citeshttps://doi.org/10.1016/j.tree.2006.10.002openalex-snapshot
The supermatrix approach to systematics
inferred← citeshttps://doi.org/10.1016/j.tree.2006.10.004openalex-snapshot
Model use in phylogenetics: nine key questions
inferred← citeshttps://doi.org/10.1016/j.ympev.2004.09.001openalex-snapshot
Strange bayes indeed: uniform topological priors imply non-uniform clade priors
inferred← citeshttps://doi.org/10.1016/j.ympev.2005.04.008openalex-snapshot
Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails
inferred← citeshttps://doi.org/10.1016/j.ympev.2011.08.008openalex-snapshot
Phylogeny, biogeography, and display evolution in the tree and brush lizard genus Urosaurus (Squamata: Phrynosomatidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.08.021openalex-snapshot
A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses
inferred← citeshttps://doi.org/10.1016/j.ympev.2016.05.001openalex-snapshot
On simulated annealing phase transitions in phylogeny reconstruction
inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107327openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/s0040-5809(02)00005-9openalex-snapshot
Statistics for phylogenetic trees
inferred← citeshttps://doi.org/10.1016/s0065-308x(06)63001-7openalex-snapshot
Phylogenetic Analyses of Parasites in the New Millennium
inferred← citeshttps://doi.org/10.1016/s0748-3007(03)00029-xopenalex-snapshot
The perils of 'point-and-click' systematics
inferred← citeshttps://doi.org/10.1016/s0748-3007(03)00074-4openalex-snapshot
Data exploration in phylogenetic inference: scientific, heuristic, or neither
inferred← citeshttps://doi.org/10.1016/s1055-7903(03)00115-5openalex-snapshot
Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
inferred← citeshttps://doi.org/10.1017/cbo9781107705937openalex-snapshot
Ockham's Razors: A User's Manual
inferred← citeshttps://doi.org/10.1017/cbo9781316338797.015openalex-snapshot
Molecular data in systematics: a promise fulfilled, a future beckoning
inferred← citeshttps://doi.org/10.1017/pab.2025.10076openalex-snapshot
Bayesian inference of phylogenetic trees is not misled by correlated discrete morphological characters
inferred← citeshttps://doi.org/10.1017/s1477200007002290openalex-snapshot
Phylogeny of snakes (Serpentes): Combining morphological and molecular data in likelihood, Bayesian and parsimony analyses
inferred← citeshttps://doi.org/10.1038/44766openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/nature02917openalex-snapshot
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inferred← citeshttps://doi.org/10.1039/b910458popenalex-snapshot
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inferred← citeshttps://doi.org/10.1071/is02016openalex-snapshot
Systematics and biogeography of the family Scorpionidae (Chelicerata : Scorpiones), with a discussion on phylogenetic methods
inferred← citeshttps://doi.org/10.1071/is05020openalex-snapshot
Revision of Nicrophorus in part: new species and inferred phylogeny of the nepalensis-group based on evidence from morphology and mitochondrial DNA (Coleoptera : Silphidae : Nicrophorinae)
inferred← citeshttps://doi.org/10.1073/pnas.0901224106openalex-snapshot
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inferred← citeshttps://doi.org/10.1078/1439-6092-00023openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/106351500750049879openalex-snapshot
Tree Robustness and Clade Significance
inferred← citeshttps://doi.org/10.1080/10635150118268openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/10635150119615openalex-snapshot
Philosophical Conjectures and Their Refutation
inferred← citeshttps://doi.org/10.1080/106351501753462876openalex-snapshot
A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data
inferred← citeshttps://doi.org/10.1080/10635150309324openalex-snapshot
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inferred← citeshttps://doi.org/10.1080/10635150490423809openalex-snapshot
Distances that Perfectly Mislead
inferred← citeshttps://doi.org/10.1080/10635150490445788openalex-snapshot
Inconsistency of Maximum Parsimony Revisited
inferred← citeshttps://doi.org/10.1080/10635150490468657openalex-snapshot
The Contest Between Parsimony and Likelihood
inferred← citeshttps://doi.org/10.1080/10635150500431155openalex-snapshot
Are Unequal Clade Priors Problematic for Bayesian Phylogenetics?
inferred← citeshttps://doi.org/10.1080/10635150590946808openalex-snapshot
Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards
inferred← citeshttps://doi.org/10.1080/10635150600755396openalex-snapshot
The Phylogeny of Early Eureptiles: Comparing Parsimony and Bayesian Approaches in the Investigation of a Basal Fossil Clade
inferred← citeshttps://doi.org/10.1080/10635150802166046openalex-snapshot
A Bayesian Perspective on a Non-parsimonious Parsimony Model
inferred← citeshttps://doi.org/10.1080/10635150802203898openalex-snapshot
More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States
inferred← citeshttps://doi.org/10.1080/10635150802422274openalex-snapshot
Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap
inferred← citeshttps://doi.org/10.1080/11263504.2023.2287530openalex-snapshot
Disentangling the distribution of Adenostyles in the Northern Iberian Peninsula: new insights from nuclear and plastid markers
inferred← citeshttps://doi.org/10.1080/11263504.2023.2293036openalex-snapshot
Redefining the phylogenetic relationships of European Angelica (Apiaceae) species
inferred← citeshttps://doi.org/10.1080/14772019.2013.764357openalex-snapshot
Archaeopteryx, paravian phylogenetic analyses, and the use of probability-based methods for palaeontological datasets
inferred← citeshttps://doi.org/10.1086/725455openalex-snapshot
Morphological plasticity in a caddisfly that co-occurs in lakes and streams
inferred← citeshttps://doi.org/10.1089/cmb.1998.5.391openalex-snapshot
Better Methods for Solving Parsimony and Compatibility
inferred← citeshttps://doi.org/10.1089/cmb.2006.0101openalex-snapshot
Reconstruction of Ancestral Genomic Sequences Using Likelihood
inferred← citeshttps://doi.org/10.1089/cmb.2013.0134openalex-snapshot
Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming
inferred← citeshttps://doi.org/10.1089/cmb.2021.0383openalex-snapshot
Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling
inferred← citeshttps://doi.org/10.1089/cmb.2022.0141openalex-snapshot
Determining Significant Correlation Between Pairs of Extant Characters in a Small Parsimony Framework
inferred← citeshttps://doi.org/10.1089/cmb.2024.0710openalex-snapshot
Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.001.0001openalex-snapshot
Computational Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0004openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0005openalex-snapshot
Dedication
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.002.0006openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0001openalex-snapshot
Models of nucleotide substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0002openalex-snapshot
Models of amino acid and codon substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0003openalex-snapshot
Phylogeny reconstruction: overview
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0004openalex-snapshot
Maximum likelihood methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0005openalex-snapshot
Bayesian methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0006openalex-snapshot
Comparison of methods and tests on trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0007openalex-snapshot
Molecular clock and estimation of species divergence times
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0008openalex-snapshot
Neutral and adaptive protein evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0009openalex-snapshot
Simulating molecular evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.003.0010openalex-snapshot
Perspectives
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198567028.005.0001openalex-snapshot
Appendices
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199297306.003.0006openalex-snapshot
Parsimony and the problem of inapplicables in sequence data
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199297306.003.0008openalex-snapshot
Parsimony and Bayesian phylogenetics
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0004openalex-snapshot
Foreword
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.002.0005openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0001openalex-snapshot
Models of nucleotide substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0002openalex-snapshot
Models of amino acid and codon substitution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0003openalex-snapshot
Phylogeny reconstruction: overview
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0004openalex-snapshot
Maximum likelihood methods
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0005openalex-snapshot
Comparison of phylogenetic methods and tests on trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0006openalex-snapshot
Bayesian theory
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0007openalex-snapshot
Bayesian computation (MCMC)
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0008openalex-snapshot
Bayesian phylogenetics
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0009openalex-snapshot
Coalescent theory and species trees
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0010openalex-snapshot
Molecular clock and estimation of species divergence times
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0011openalex-snapshot
Neutral and adaptive protein evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0012openalex-snapshot
Simulating molecular evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780199602605.003.0013openalex-snapshot
Appendices
inferred← citeshttps://doi.org/10.1093/aob/mcae084openalex-snapshot
Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa444openalex-snapshot
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
inferred← citeshttps://doi.org/10.1093/bioinformatics/bti1027openalex-snapshot
Maximum likelihood of evolutionary trees: hardness and approximation
inferred← citeshttps://doi.org/10.1093/bioinformatics/bti191openalex-snapshot
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
inferred← citeshttps://doi.org/10.1093/evolut/qpae166openalex-snapshot
Correlated evolution of categorical characters under a simple model
inferred← citeshttps://doi.org/10.1093/gbe/evr013openalex-snapshot
Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction
inferred← citeshttps://doi.org/10.1093/isd/ixz006openalex-snapshot
A Systematist’s Guide to Estimating Bayesian Phylogenies From Morphological Data
inferred← citeshttps://doi.org/10.1093/molbev/msi091openalex-snapshot
Complex Spliceosomal Organization Ancestral to Extant Eukaryotes
inferred← citeshttps://doi.org/10.1093/molbev/msm274openalex-snapshot
Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis
inferred← citeshttps://doi.org/10.1093/molbev/msp184openalex-snapshot
General Heterotachy and Distance Method Adjustments
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026252openalex-snapshot
Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026364openalex-snapshot
Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/45.4.596openalex-snapshot
Corrected Parsimony, Minimum Evolution, and Hadamard Conjugations
inferred← citeshttps://doi.org/10.1093/sysbio/syaa031openalex-snapshot
Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data
inferred← citeshttps://doi.org/10.1093/sysbio/syab001openalex-snapshot
Long Branch Attraction Biases in Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/syab069openalex-snapshot
Accuracy in Near-Perfect Virus Phylogenies
inferred← citeshttps://doi.org/10.1093/sysbio/syad063openalex-snapshot
Is Over-parameterization a Problem for Profile Mixture Models?
inferred← citeshttps://doi.org/10.1093/sysbio/syae055openalex-snapshot
Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations
inferred← citeshttps://doi.org/10.1093/sysbio/syae064openalex-snapshot
How to Validate a Bayesian Evolutionary Model
inferred← citeshttps://doi.org/10.1093/sysbio/syaf050openalex-snapshot
Practical Guide and Review of Fossil Tip-Dating in Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/syp077openalex-snapshot
New Heuristic Methods for Joint Species Delimitation and Species Tree Inference
inferred← citeshttps://doi.org/10.1093/sysbio/syp079openalex-snapshot
Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites
inferred← citeshttps://doi.org/10.1093/sysbio/syq028openalex-snapshot
The Akaike Information Criterion Will Not Choose the No Common Mechanism Model
inferred← citeshttps://doi.org/10.1093/sysbio/syq069openalex-snapshot
Can We Avoid “SIN” in the House of “No Common Mechanism”?
inferred← citeshttps://doi.org/10.1093/sysbio/syq089openalex-snapshot
Biologically Inspired Phylogenetic Models Strongly Outperform the No Common Mechanism Model
inferred← citeshttps://doi.org/10.1093/sysbio/syr095openalex-snapshot
SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees
inferred← citeshttps://doi.org/10.1093/sysbio/sys064openalex-snapshot
When Do Phylogenetic Mixture Models Mimic Other Phylogenetic Models?
inferred← citeshttps://doi.org/10.1093/sysbio/syt059openalex-snapshot
Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees
inferred← citeshttps://doi.org/10.1093/sysbio/syu010openalex-snapshot
Predicting the Ancestral Character Changes in a Tree is Typically Easier than Predicting the Root State
inferred← citeshttps://doi.org/10.1093/sysbio/syu064openalex-snapshot
Popperian Corroboration and Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/syv005openalex-snapshot
Ancestral State Reconstruction, Rate Heterogeneity, and the Evolution of Reptile Viviparity
inferred← citeshttps://doi.org/10.1093/sysbio/syv008openalex-snapshot
Circumstances in Which Parsimony but not Compatibility will be Provably Misleading
inferred← citeshttps://doi.org/10.1093/sysbio/syv016openalex-snapshot
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
inferred← citeshttps://doi.org/10.1093/sysbio/syy061openalex-snapshot
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods
inferred← citeshttps://doi.org/10.1093/sysbio/syy071openalex-snapshot
Serial Homology and Correlated Characters in Morphological Phylogenetics: Modeling the Evolution of Dental Crests in Placentals
inferred← citeshttps://doi.org/10.1093/sysbio/syy077openalex-snapshot
Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model
inferred← citeshttps://doi.org/10.1093/ve/veab073openalex-snapshot
Decomposing the sources of SARS-CoV-2 fitness variation in the United States
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlac041openalex-snapshot
Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlz088openalex-snapshot
Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)
inferred← citeshttps://doi.org/10.1098/rsif.2016.0363openalex-snapshot
Progress, pitfalls and parallel universes: a history of insect phylogenetics
inferred← citeshttps://doi.org/10.1101/2023.01.24.525451openalex-snapshot
The Impact of Multiple Sequence Alignment Error on Phylogenetic Estimation under Variable-Across-Phylogeny Substitution Models
inferred← citeshttps://doi.org/10.1101/2025.04.22.650124openalex-snapshot
State Space Misspecification in Morphological Phylogenetics: A Pitfall for Models and Parsimony Alike
inferred← citeshttps://doi.org/10.1101/640334openalex-snapshot
Complex ecological phenotypes on phylogenetic trees: a hidden Markov model for comparative analysis of multivariate count data
inferred← citeshttps://doi.org/10.1109/ipdps.2004.1303212openalex-snapshot
New fast and accurate heuristics for inference of large phylogenetic trees
inferred← citeshttps://doi.org/10.1109/tcbb.2004.34openalex-snapshot
Unidentifiable divergence times in rates-across-sites models
inferred← citeshttps://doi.org/10.1109/tcbb.2006.4openalex-snapshot
A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood Is Hard
inferred← citeshttps://doi.org/10.1111/1467-9868.00354openalex-snapshot
A Model Selection Approach for the Identification of Quantitative Trait Loci in Experimental Crosses
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