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Phylogenetic analysis using parsimony and likelihood methods
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Relative Efficiencies of the Maximum Likelihood, Maximum Parsimony, and Neighbor-Joining Methods for Estimating Protein Phylogeny
inferredcites →https://doi.org/10.1007/bf00160154openalex-snapshot
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
inferredcites →https://doi.org/10.1007/bf00160518openalex-snapshot
Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
inferredcites →https://doi.org/10.1007/bf00163810openalex-snapshot
Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant
inferredcites →https://doi.org/10.1007/bf00178256openalex-snapshot
Estimating the pattern of nucleotide substitution
inferredcites →https://doi.org/10.1007/bf01731581openalex-snapshot
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
inferredcites →https://doi.org/10.1007/bf01734101openalex-snapshot
Mitochondrial DNA sequences of primates: Tempo and mode of evolution
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/bf02099932openalex-snapshot
Robustness of maximum likelihood tree estimation against different patterns of base substitutions
inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
inferredcites →https://doi.org/10.1007/bf02109483openalex-snapshot
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
inferredcites →https://doi.org/10.1016/0047-2484(88)90069-3openalex-snapshot
Molecules and morphology in evolution: Conflict or compromise?
inferredcites →https://doi.org/10.1016/0305-4403(76)90038-8openalex-snapshot
Human evolutionary trees
inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot
Evolution of Protein Molecules
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The Advanced Theory of Statistics, Vol. 3
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Univariate Discrete Distributions (2nd Ed.)
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A space-time process model for the evolution of DNA sequences.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040020openalex-snapshot
A Simple Method to Improve the Reliability of Tree Reconstructions
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040082openalex-snapshot
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040108openalex-snapshot
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040109openalex-snapshot
Estimation of evolutionary distance for reconstructing molecular phylogenetic trees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040112openalex-snapshot
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040126openalex-snapshot
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040152openalex-snapshot
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040183openalex-snapshot
Success of maximum likelihood phylogeny inference in the four-taxon case.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040432openalex-snapshot
Accuracy of phylogenetic trees estimated from DNA sequence data.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040572openalex-snapshot
Relative Efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040588openalex-snapshot
Limitations of the evolutionary parsimony method of phylogenetic analysis.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040740openalex-snapshot
The consistency of several phylogeny-inference methods under varying evolutionary rates.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040782openalex-snapshot
Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.
inferredcites →https://doi.org/10.1093/sysbio/20.4.406openalex-snapshot
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
inferredcites →https://doi.org/10.1093/sysbio/22.3.240openalex-snapshot
Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
inferredcites →https://doi.org/10.1093/sysbio/22.3.250openalex-snapshot
A Probability Model for Inferring Evolutionary Trees
inferredcites →https://doi.org/10.1093/sysbio/24.2.233openalex-snapshot
Karl R. Popper, Systematics, and Classification: A Reply to Walter Bock and Other Evolutionary Taxonomists
inferredcites →https://doi.org/10.1093/sysbio/26.1.77openalex-snapshot
Phylogenetic Analysis Under Dollo's Law
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
inferredcites →https://doi.org/10.1093/sysbio/42.2.113openalex-snapshot
Inconsistency of the Maximum-Parsimony Method: The Case of Five Taxa with a Molecular Clock
inferredcites →https://doi.org/10.1093/sysbio/42.2.193openalex-snapshot
Is There Something Wrong with the Bootstrap on Phylogenies? A Reply to Hillis and Bull
inferredcites →https://doi.org/10.1093/sysbio/42.3.247openalex-snapshot
Success of Phylogenetic Methods in the Four-Taxon Case
inferredcites →https://doi.org/10.1093/sysbio/43.3.329openalex-snapshot
Statistical Properties of the Maximum Likelihood Method of Phylogenetic Estimation and Comparison With Distance Matrix Methods
inferredcites →https://doi.org/10.1093/sysbio/43.3.424openalex-snapshot
What Is the Bootstrap Technique?
inferredcites →https://doi.org/10.1093/sysbio/44.3.384openalex-snapshot
Maximum Likelihood Trees from DNA Sequences: A Peculiar Statistical Estimation Problem
inferredcites →https://doi.org/10.1098/rspb.1985.0096openalex-snapshot
Evolutionary trees from nucleic acid and protein sequences
inferredcites →https://doi.org/10.1101/sqb.1987.052.01.093openalex-snapshot
Reliability of Evolutionary Trees
inferredcites →https://doi.org/10.1111/j.1558-5646.1965.tb01722.xopenalex-snapshot
A METHOD FOR DEDUCING BRANCHING SEQUENCES IN PHYLOGENY
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PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES
inferredcites →https://doi.org/10.1111/j.1558-5646.1985.tb00420.xopenalex-snapshot
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
inferredcites →https://doi.org/10.1111/j.2517-6161.1970.tb00828.xopenalex-snapshot
Estimation of the Branch Points of a Branching Diffusion Process
inferredcites →https://doi.org/10.1136/jcp.16.2.185-aopenalex-snapshot
PROTIDES OF THE BIOLOGICAL FLUIDS
inferredcites →https://doi.org/10.1146/annurev.ge.22.120188.002513openalex-snapshot
PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY
inferredcites →https://doi.org/10.1198/tech.2006.s421openalex-snapshot
Univariate Discrete Distributions
inferredcites →https://doi.org/10.1214/aoms/1177729952openalex-snapshot
Note on the Consistency of the Maximum Likelihood Estimate
inferredcites →https://doi.org/10.2307/1402106openalex-snapshot
Classical and Contagious Discrete Distributions
inferredcites →https://doi.org/10.2307/2186094openalex-snapshot
Reconstructing the Past: Parsimony, Evolution, and Inference.
inferredcites →https://doi.org/10.2307/2412074openalex-snapshot
Atlas of Protein Sequence and Structure, 1966.
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/10.2307/2412304openalex-snapshot
Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
inferredcites →https://doi.org/10.2307/2412305openalex-snapshot
A Probability Model for Inferring Evolutionary Trees
inferredcites →https://doi.org/10.2307/2412764openalex-snapshot
Karl R. Popper, Systematics, and Classification: A Reply to Walter Bock and Other Evolutionary Taxonomists
inferredcites →https://doi.org/10.2307/2412867openalex-snapshot
Phylogenetic Analysis Under Dollo's Law
inferredcites →https://doi.org/10.2307/2412923openalex-snapshot
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
inferredcites →https://doi.org/10.2307/2413121openalex-snapshot
Parsimony and Likelihood: An Exchange
inferredcites →https://doi.org/10.2307/2529676openalex-snapshot
Minimum Mutation Fits to a Given Tree
inferredcites →https://doi.org/10.2307/2532170openalex-snapshot
Reconstructing the Past: Parsimony, Evolution, and Inference.
inferredcites →https://doi.org/10.2307/2992293openalex-snapshot
Reconstructing the Past: Parsimony, Evolution, and Inference.
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
inferredcites →https://doi.org/10.3891/acta.chem.scand.17s-0009openalex-snapshot
Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life.
inferredcites →https://doi.org/10.5691/jjb.5.1openalex-snapshot
MAXIMUM LIKELIHOOD METHOD OF PHYLOGENETIC INFERENCE FROM DNA SEQUENCE DATA
inferredcites →https://doi.org/10.5860/choice.39-2183openalex-snapshot
MacClade 4.0: analysis of phylogeny and character evolution
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Lophiostomataceae (Dothideomycetes): Introducing Lophiostoma khanzada-kirgizbaeva sp. nov. and Paucispora xishanensis sp. nov.
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PAML (Phylogenetic Analysis by Maximum Likelihood)
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Conventional Phylogenetics and Systematics
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Reconstructing phylogenies from allozyme data: comparing method performance with congruence
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Probabilism and Phylogenetic Inference
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Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case
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Rapid Speciation, Morphological Evolution, and Adaptation to Extreme Environments in South African Sand Lizards (Meroles) as Revealed by Mitochondrial Gene Sequences
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Molecular Phylogenetics at the Felsenstein Zone: Approaching the Strepsiptera Problem Using 5.8S and 28S rDNA Sequences
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Molecular Evolutionary Relationships in the Avian GenusAnthus(Pipits: Motacillidae)
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Dynamically Heterogenous Partitions and Phylogenetic Inference: An Evaluation of Analytical Strategies with Cytochrome b and ND6 Gene Sequences in Cranes
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Phylogeny of “Oxycanus” Lineages of Hepialid Moths from New Zealand Inferred from Sequence Variation in the mtDNA COI and II Gene Regions
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Phylogenetic Inferences from Molecular Sequences: Review and Critique
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The statistical approach to molecular phylogeny: Evidence for a nonhyperthermophilic common ancestor
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Tree and Network Building
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Patterns of Sequence Evolution and Implications for Parsimony Analysis of Chloroplast DNA
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Molecular Phylogenetics: Testing Evolutionary Hypotheses
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Underlying Principles and Key Methods for Infectious Disease Molecular Epidemiology
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MrBayes for Phylogenetic Inference Using Protein Data on a GPU Cluster
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5 Quantitative Approaches to Phylogenetics
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Quantitative Approaches to Phylogenetics
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Modeling the Avian Influenza H5N1 Virus Infection in Human and Analyzing Its Evolution
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Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
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Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders
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A Novel Approach to Phylogeny Reconstruction from Protein Sequences
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PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades
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Spatial Autocorrelation of Amino Acid Replacement Rates in the Vasopressin Receptor Family
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Felsenstein Phylogenetic Likelihood
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Deformity Index: A Semi-Reference Clade-Based Quality Metric of Phylogenetic Trees
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Origin and diversification of Thymelaea (Thymelaeaceae): inferences from a phylogenetic study based on ITS (rDNA) sequences
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Hymenobacter negativus sp. nov., bacteria isolated from mountain soil collected in South Korea
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Hymenobacter puniceus sp. nov., radiation resistant bacteria isolated from soil in South Korea
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Using multiple analytical methods to improve phylogenetic hypotheses in Minaria (Apocynaceae)
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Synthetic gene technology: Applications to ancestral gene reconstruction and structure-function studies of receptors
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Recreating ancestral proteins
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Counting mutations by parsimony and estimation of mutation rate variation across nucleotide sites —a simulation study
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Evolution of Eukaryotic Cell Cycle Regulation
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A molecular phylogeny of African kestrels with reference to divergence across the Indian Ocean
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Searching Biological Databases Using Biolinguistic Methods
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Rhabdias glaurungisp. nov. (Nematoda: Rhabdiasidae), parasite ofScinaxgr.ruber(Laurenti, 1768) (Anura: Hylidae), from the Brazilian Amazon
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inferred← citeshttps://doi.org/10.1017/s0953756201004269openalex-snapshot
Molecular phylogeny of the Bacidiaceae (Lecanorales, lichenized Ascomycota)
inferred← citeshttps://doi.org/10.1023/a:1027314112438openalex-snapshot
Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics
inferred← citeshttps://doi.org/10.1038/nrg3186openalex-snapshot
Molecular phylogenetics: principles and practice
inferred← citeshttps://doi.org/10.1038/nsmb.1529openalex-snapshot
Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors
inferred← citeshttps://doi.org/10.1038/s41559-022-01956-zopenalex-snapshot
Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
inferred← citeshttps://doi.org/10.1038/s41598-017-17392-0openalex-snapshot
Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential
inferred← citeshttps://doi.org/10.1038/s41598-020-64647-4openalex-snapshot
Accuracy of ancestral state reconstruction for non-neutral traits
inferred← citeshttps://doi.org/10.1038/s41598-021-85008-9openalex-snapshot
Phylogenetic prospecting for cryptic species of the genus Merluccius (Actinopterygii: Merlucciidae)
inferred← citeshttps://doi.org/10.1038/s41598-023-42017-0openalex-snapshot
Selenobaculum gbiensis gen. nov. sp. nov., a new bacterium isolated from the gut microbiota of a patient with Crohn’s disease
inferred← citeshttps://doi.org/10.1039/d5ra06679dopenalex-snapshot
New insights into enhancement of cadmium biosorption from industrial wastewater through Chlorella sorokiniana HMYA based thin-film
inferred← citeshttps://doi.org/10.1046/j.1365-294x.1999.00793.xopenalex-snapshot
Phylogeography of the California mountain kingsnake,Lampropeltis zonata(Colubridae)
inferred← citeshttps://doi.org/10.1046/j.1420-9101.1999.00070.xopenalex-snapshot
Circularity, evolution, systematics … and circularity
inferred← citeshttps://doi.org/10.1046/j.1463-6409.2000.00045.xopenalex-snapshot
Phylogenetic position of the Tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi
inferred← citeshttps://doi.org/10.1046/j.1463-6409.2002.00101.xopenalex-snapshot
Divergent evolution, hierarchy and cladistics
inferred← citeshttps://doi.org/10.1046/j.1529-8817.2000.99106.xopenalex-snapshot
PHYLOGENY OF THE CONJUGATING GREEN ALGAE (ZYGNEMOPHYCEAE) BASED ON rbc L SEQUENCES
inferred← citeshttps://doi.org/10.1073/pnas.0409159102openalex-snapshot
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
inferred← citeshttps://doi.org/10.1073/pnas.220427497openalex-snapshot
Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny
inferred← citeshttps://doi.org/10.1073/pnas.95.21.12390openalex-snapshot
The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small
inferred← citeshttps://doi.org/10.1080/00275514.2018.1548863openalex-snapshot
Multigene phylogenetic and morphological evidence for seven new species of Aquanectria and Gliocladiopsis (Ascomycota, Hypocreales) from tropical areas
inferred← citeshttps://doi.org/10.1080/0028825x.2023.2272957openalex-snapshot
Sexual morph of Allophoma tropica and Didymella coffeae-arabicae ( Didymellaceae , Pleosporales , Dothidiomycetes ), including novel host records from leaf litter in Thailand
inferred← citeshttps://doi.org/10.1080/02664763.2013.785652openalex-snapshot
Bayesian factor models in characterizing molecular adaptation
inferred← citeshttps://doi.org/10.1080/03014223.2000.9518203openalex-snapshot
Phylogenetic relationships within the genus Wiseana (Lepidoptera: Hepialidae)
inferred← citeshttps://doi.org/10.1080/10635150050207410openalex-snapshot
Is There a Justification for Differential a Priori Weighting in Coding Sequences? A Case Study from rbcL and Apocynaceae s.l.
inferred← citeshttps://doi.org/10.1080/10635150050207447openalex-snapshot
War of the Iguanas: Conflicting Molecular and Morphological Phylogenies and Long-Branch Attraction in Iguanid Lizards
inferred← citeshttps://doi.org/10.1080/106351500750049879openalex-snapshot
Tree Robustness and Clade Significance
inferred← citeshttps://doi.org/10.1080/10635150116786openalex-snapshot
Exploring Among-Site Rate Variation Models in a Maximum Likelihood Framework Using Empirical Data: Effects of Model Assumptions on Estimates of Topology, Branch Lengths, and Bootstrap Support
inferred← citeshttps://doi.org/10.1080/10635150117959openalex-snapshot
Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods
inferred← citeshttps://doi.org/10.1080/10635150118469openalex-snapshot
Selecting the Best-Fit Model of Nucleotide Substitution
inferred← citeshttps://doi.org/10.1080/106351501753328839openalex-snapshot
Maximum Likelihood Estimation of Phylogenetic Trees Is Consistent When Substitution Rates Vary According to the Invariable Sites plus Gamma Distribution
inferred← citeshttps://doi.org/10.1080/106351501753462821openalex-snapshot
Phylogeny of Saxifragales (Angiosperms, Eudicots): Analysis of a Rapid, Ancient Radiation
inferred← citeshttps://doi.org/10.1080/106351502753475899openalex-snapshot
A Molecular Phylogenetic Study of the Palmae (Arecaceae) Based on atpB, rbcL, and 18S nrDNA Sequences
inferred← citeshttps://doi.org/10.1080/10635150290102339openalex-snapshot
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
inferred← citeshttps://doi.org/10.1080/10635150309324openalex-snapshot
Failed Refutations: Further Comments on Parsimony and Likelihood Methods and Their Relationship to Popper's Degree of Corroboration
inferred← citeshttps://doi.org/10.1080/10635150701499563openalex-snapshot
Experimental Design Criteria in Phylogenetics: Where to Add Taxa
inferred← citeshttps://doi.org/10.1080/10635150802422324openalex-snapshot
A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences
inferred← citeshttps://doi.org/10.1080/106351598260842openalex-snapshot
Archiving Molecular Phylogenetic Alignments as NEXUS Files
inferred← citeshttps://doi.org/10.1080/106351598261021openalex-snapshot
Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators
inferred← citeshttps://doi.org/10.1080/106351598261067openalex-snapshot
On the Best Evolutionary Rate for Phylogenetic Analysis
inferred← citeshttps://doi.org/10.1080/10635159950127411openalex-snapshot
Phylogenetic Relationships Among the Phrynosomatid Sand Lizards Inferred from Mitochondrial DNA Sequences Generated by Heterogeneous Evolutionary Processes
inferred← citeshttps://doi.org/10.1080/15572536.2004.11833027openalex-snapshot
New Approach to an Old Problem: Incorporating Signal from Gap-Rich Regions of ITS and rDNA Large Subunit into Phylogenetic Analyses to Resolve the Peltigera canina Species Complex
inferred← citeshttps://doi.org/10.1080/22221751.2019.1663712openalex-snapshot
Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016–2018
inferred← citeshttps://doi.org/10.1086/653661openalex-snapshot
Parental Care Trade‐Offs and Life‐History Relationships in Insects
inferred← citeshttps://doi.org/10.1086/739496openalex-snapshot
Tracing the History of Angiosperm Systematics through Liliales and Asparagales
inferred← citeshttps://doi.org/10.1088/1751-8121/ab305bopenalex-snapshot
Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
inferred← citeshttps://doi.org/10.1089/1066527041410472openalex-snapshot
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis
inferred← citeshttps://doi.org/10.1089/cmb.2015.0146openalex-snapshot
Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference
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/9780198567028.003.0001openalex-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/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/9780199602605.003.0001openalex-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/bib/bbq079openalex-snapshot
Result verification, code verification and computation of support values in phylogenetics
inferred← citeshttps://doi.org/10.1093/bioinformatics/btg043openalex-snapshot
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees
inferred← citeshttps://doi.org/10.1093/bioinformatics/btg295openalex-snapshot
A new sequence distance measure for phylogenetic tree construction
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq532openalex-snapshot
Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq549openalex-snapshot
GLOOME: gain loss mapping engine
inferred← citeshttps://doi.org/10.1093/bioinformatics/bts396openalex-snapshot
Uncovering the co-evolutionary network among prokaryotic genes
inferred← citeshttps://doi.org/10.1093/condor/104.4.740openalex-snapshot
PHYLOGENETIC RELATIONSHIPS OF THE WRENTIT BASED ON MITOCHONDRIAL CYTOCHROME b SEQUENCES
inferred← citeshttps://doi.org/10.1093/gbe/evr101openalex-snapshot
Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study
inferred← citeshttps://doi.org/10.1093/gbe/evv134openalex-snapshot
The Highly Reduced Plastome of MycoheterotrophicSciaphila(Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection
inferred← citeshttps://doi.org/10.1093/gigascience/giab036openalex-snapshot
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations
inferred← citeshttps://doi.org/10.1093/molbev/msaa166openalex-snapshot
A Simulation Study to Examine the Information Content in Phylogenomic Data Sets under the Multispecies Coalescent Model
inferred← citeshttps://doi.org/10.1093/molbev/msab009openalex-snapshot
Complexity of the simplest species tree problem
inferred← citeshttps://doi.org/10.1093/molbev/msg040openalex-snapshot
Molecular Phylogeny of Early Vertebrates: Monophyly of the Agnathans as Revealed by Sequences of 35 Genes
inferred← citeshttps://doi.org/10.1093/molbev/msh198openalex-snapshot
Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference
inferred← citeshttps://doi.org/10.1093/molbev/msn162openalex-snapshot
Recent Origins of Sperm Genes in Drosophila
inferred← citeshttps://doi.org/10.1093/molbev/msq333openalex-snapshot
The Complexity Hypothesis Revisited: Connectivity Rather Than Function Constitutes a Barrier to Horizontal Gene Transfer
inferred← citeshttps://doi.org/10.1093/molbev/msu340openalex-snapshot
Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003907openalex-snapshot
Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003969openalex-snapshot
Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004094openalex-snapshot
The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025613openalex-snapshot
Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025691openalex-snapshot
When is it safe to use an oversimplified substitution model in tree- making?
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025866openalex-snapshot
Nucleotide Substitution Models and Estimation of Phylogeny
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025991openalex-snapshot
Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026045openalex-snapshot
The Effect of Taxon Sampling on Estimating Rate Heterogeneity Parameters of Maximum-Likelihood Models
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026171openalex-snapshot
Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026286openalex-snapshot
Assessing an Unknown Evolutionary Process: Effect of Increasing Site-Specific Knowledge Through Taxon Addition
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/oxfordjournals.molbev.a026405openalex-snapshot
Bias in Phylogenetic Reconstruction of Vertebrate Rhodopsin Sequences
inferred← citeshttps://doi.org/10.1093/sysbio/46.2.354openalex-snapshot
On the Consistency of Maximum Likelihood Estimation of Phylogenetic Trees from Nucleotide Sequences
inferred← citeshttps://doi.org/10.1093/sysbio/46.3.426openalex-snapshot
Phylogeography and Molecular Systematics of the Peromyscus Aztecus Species Group (Rodentia: Muridae) Inferred Using Parsimony and Likelihood
inferred← citeshttps://doi.org/10.1093/sysbio/46.4.751openalex-snapshot
Process Partitions, Congruence, and the Independence of Characters: Inferring Relationships among Closely Related Hawaiian Drosophila from Multiple Gene Regions
inferred← citeshttps://doi.org/10.1093/sysbio/syaa100openalex-snapshot
The Asymptotic Behavior of Bootstrap Support Values in Molecular Phylogenetics
inferred← citeshttps://doi.org/10.1093/sysbio/syp056openalex-snapshot
The Use and Validity of Composite Taxa in Phylogenetic Analysis
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