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Approaches for Assessing Phylogenetic Accuracy
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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On the Foundations of Statistical Inference
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Statistical tests of models of DNA substitution
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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Congruency of phylogenies derived from different proteins
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Accuracy of estimated phylogenetic trees from molecular data
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Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
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Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data
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Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences
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Mutation pattern of human immunodeficiency virus genes
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Estimation of hominoid phylogeny from a DNA hybridization data set
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Calibrating the bootstrap test of monophyly
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Reconstructing evolution of sequences subject to recombination using parsimony
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[34] Analysis of DNA sequence data: Phylogenetic inference
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Progress with methods for constructing evolutionary trees
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Reconstruction of evolutionary trees
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A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree
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Better Bootstrap Confidence Intervals
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The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods
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Bootstrap Confidence Intervals for a Class of Parametric Problems
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A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping. I. Basic Theory and an Analysis of Alcohol Dehydrogenase Activity in Drosophila
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Signal, Noise, and Reliability in Molecular Phylogenetic Analyses
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Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis.
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Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.
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Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation.
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A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree.
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A statistical test of phylogenies estimated from sequence data.
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The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies.
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The consistency of several phylogeny-inference methods under varying evolutionary rates.
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Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method.
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Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.
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Consensus Techniques and the Comparison of Taxonomic Trees
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Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
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Cases in which Parsimony or Compatibility Methods will be Positively Misleading
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Monophyly of the Tyrannidae (Aves): Comparison of Morphology and DNA
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The Use of Tree Comparison Metrics
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Detecting Internal Inconsistencies in Distance Data
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Tree-Length Distribution Skewness: An Indicator of Phylogenetic Information
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Cladistic Permutation Tests for Monophyly and Nonmonophyly
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Experimental Approaches to Phylogenetic Analysis
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Success of Phylogenetic Methods in the Four-Taxon Case
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Improving the Accuracy of Phylogenetic Estimation by Combining Different Methods
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Partitioning and Combining Data in Phylogenetic Analysis
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A Congruence Test of Reliability Using Linked Mitochondrial DNA Sequences
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Is Character Weighting a Panacea for the Problem of Data Heterogeneity in Phylogenetic Analysis?
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Performance of Phylogenetic Methods in Simulation
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Statistical Tests of DNA Phylogenies
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Testing Species Phylogenies and Phylogenetic Methods with Congruence
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CONSENSUS CLADOGRAMS AND GENERAL CLASSIFICATIONS
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TESTING METHODS OF EVOLUTIONARY TREE CONSTRUCTION
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COMBINABLE COMPONENT CONSENSUS
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COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE
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SKEWNESS AND PERMUTATION
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PHYLOGENETIC INFERENCE FROM RESTRICTION ENDONUCLEASE CLEAVAGE SITE MAPS WITH PARTICULAR REFERENCE TO THE EVOLUTION OF HUMANS AND THE APES
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
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THE LIMITS OF AMINO ACID SEQUENCE DATA IN ANGIOSPERM PHYLOGENETIC RECONSTRUCTION
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PHYLOGENIES OF PLANT FAMILIES: A DEMONSTRATION OF PHYLOGENETIC RANDOMNESS IN DNA SEQUENCE DATA DERIVED FROM PROTEINS
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ACCURACY OF ESTIMATED PHYLOGENIES: EFFECTS OF TREE TOPOLOGY AND EVOLUTIONARY MODEL
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COMPARISONS OF OBSERVED PHYLOGENETIC TOPOLOGIES WITH NULL EXPECTATIONS AMONG THREE MONOPHYLETIC LINEAGES
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Experimental Phylogenetics: Generation of a Known Phylogeny
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Gene Trees and the Origins of Inbred Strains of Mice
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Molecular Epidemiology of HIV Transmission in a Dental Practice
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Evolution in Inbred Strains of Mice Appears Rapid
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Application and Accuracy of Molecular Phylogenies
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Parsimony in Systematics: Biological and Statistical Issues
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MOLECULAR VERSUS MORPHOLOGICAL APPROACHES TO SYSTEMATICS
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Congruence Between Molecular and Morphological Phylogenies
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PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY
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Statistical Methods for Meta-Analysis
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Statistical Methods and Scientific Inference.
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Phylogenetic Relationships of Dipsacales Based on rbcL Sequences
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A Framework for the Quantitative Study of Evolutionary Trees
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An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
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Primary, Secondary, and Meta-Analysis of Research
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A few logs suffice to build (almost) all trees (I)
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Molecular Phylogeny and Evolution
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Probabilism and Phylogenetic Inference
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Correlation of Functional Domains and Rates of Nucleotide Substitution in Cytochromeb
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A Survey of Homeobox Genes inChaetopterus variopedatusand Analysis of Polychaete Homeodomains
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Consistency, Characters, and the Likelihood of Correct Phylogenetic Inference
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Molecular Phylogeny and Evolutionary Divergence of North American Biological Species ofArmillaria
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Phylogenetic Relationships among the Microgastroid Wasps (Hymenoptera: Braconidae): Combined Analysis of 16S and 28S rDNA Genes and Morphological Data
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The Major Opsin in Bees (Insecta: Hymenoptera): A Promising Nuclear Gene for Higher Level Phylogenetics
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Polyphyly and Convergent Morphological Evolution in Commelinales and Commelinidae: Evidence from rbcL Sequence Data
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Phylogenetic Relationships within the Class Anthozoa (Phylum Cnidaria) Based on Nuclear 18S rDNA Sequences
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The Impact of Parsimony Weighting Schemes on Inferred Relationships among Toucans and Neotropical Barbets (Aves: Piciformes)
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Slicing Hyperdimensional Oranges: The Geometry of Phylogenetic Estimation
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The Effect of Natural Selection on Phylogeny Reconstruction Algorithms
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Constructing big trees from short sequences
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Assessing Congruence: Empirical Examples from Molecular Data
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Maximum Likelihood as an Alternative to Parsimony for Inferring Phylogeny Using Nucleotide Sequence Data
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Kurze Einführung in die phylogenetische Analyse von molekularen Sequenzdaten
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Short Introduction to Phylogenetic Analysis of Molecular Sequence Data
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Ancestral DNA Sequence Reconstruction Using Recursive Genetic Algorithms
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Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach
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Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models
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ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks
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GASTS: Parsimony Scoring under Rearrangements
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A Phylogenetic Perspective on the Evolution of Morphological and Reproductive Characteristics in the Unionoida
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Molecular Systematics: 1994–1995
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Molecular Phylogenetic Relationships Among Angiosperms: An Overview Based on rbcL and 18S rDNA Sequences
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How to validate phylogenetic trees? A stepwise procedure
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Arthropod and annelid relationships re-examined
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Molecular Phylogenetics: Frequently Asked Questions
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The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species
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Morphometric and phylogenetic analysis of theDaviesia ulicifolia complex (Fabaceae, Mirbelieae)
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The circumscription ofHoffmannseggia (Fabaceae, Caesalpinioideae, Caesalpinieae) and its allies using morphological and cpDNA restriction site data
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Phylogenetic reconstruction of the felidae using 16S rRNA and NADH-5 mitochondrial genes
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Phylogeny and biogeographic history of hake (genus Merluccius ), inferred from mitochondrial DNA control-region sequences
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Tests of the accuracy of cladograms in Gilia (Polemoniaceae) and some other angiosperm genera
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Molecular epidemiology of African swine fever in East Africa
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Sequence Data, Phylogenetic Inference, and Implications of Downward Causation
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Molecular phylogenetics and systematics of Trigonella L. (Fabaceae) based on nuclear ribosomal ITS and chloroplast trnL intron sequences
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Molecular Systematics of Chipmunks (Neotamias) Inferred by Mitochondrial Control Region Sequences
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The evolutionary history of PDR in Brachypodium distachyon polyploids
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Dispelling five myths about hypothesis testing in biological systematics
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Phylogeny, Taxonomy, and Classification
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Systematics and Classification
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Biogeographic Analysis of Pacific Trout (Oncorhynchus mykiss) in California and Mexico Based on Mitochondrial DNA and Nuclear Microsatellites
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RECONSTRUCTING ANCESTRAL TRAIT VALUES USING SQUARED-CHANGE PARSIMONY: PLASMA OSMOLARITY AT THE ORIGIN OF AMNIOTES
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Missing data and the design of phylogenetic analyses
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A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in the reconstruction of phylogenetic relationships
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Arbitrarily amplified DNA markers as characters for phylogenetic inference
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Phylogeny of the Falconidae (Aves): a comparison of the efficacy of morphological, mitochondrial, and nuclear data
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Phylogeny of the orchid bees (Hymenoptera: Apinae: Euglossini): DNA and morphology yield equivalent patterns
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A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
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Phylogenetic relationships of egg parasitoids (Hymenoptera: Eulophidae) and correlated life history characteristics of their Neotropical Cassidinae hosts (Coleoptera, Chrysomelidae)
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Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny
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Phylogenetic relationships of Ruteae (Rutaceae): New evidence from the chloroplast genome and comparisons with non-molecular data
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The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae
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Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling
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Retrieving a mitogenomic mammal tree using composite taxa
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Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes
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Multi-locus species tree for the Amazonian peacock basses (Cichlidae: Cichla): Emergent phylogenetic signal despite limited nuclear variation
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RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas
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The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species
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A comparison of stilbene and chalcone synthases including a new stilbene synthase gene from Vitis riparia cv. Gloire de Montpellier
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Morphological approaches to measuring biodiversity
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Are big trees indeed easy?
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Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining
inferred← citeshttps://doi.org/10.1016/s0304-3975(99)00028-6openalex-snapshot
A few logs suffice to build (almost) all trees: Part II
inferred← citeshttps://doi.org/10.1016/s0305-1978(01)00102-8openalex-snapshot
Phylogenetic relationships of the Rhizophoraceae in China based on sequences of the chloroplast gene matK and the internal transcribed spacer regions of nuclear ribosomal DNA and combined data set
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(02)00371-8openalex-snapshot
Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa
inferred← citeshttps://doi.org/10.1017/s0022336000043511openalex-snapshot
Resolution, sampling, higher taxa and assumptions in stratocladistic analysis
inferred← citeshttps://doi.org/10.1017/s108933260000187xopenalex-snapshot
Probabilistic Phylogenetic Inference in the Fossil Record: Current and Future Applications
inferred← citeshttps://doi.org/10.1017/s1748499518000337openalex-snapshot
Analysis of financial events under an assumption of complexity
inferred← citeshttps://doi.org/10.1038/s41598-017-13236-zopenalex-snapshot
Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses
inferred← citeshttps://doi.org/10.1038/sj.gene.6363648openalex-snapshot
Taxonomic hierarchy of HLA class I allele sequences
inferred← citeshttps://doi.org/10.1046/j.1096-3642.2002.00005.xopenalex-snapshot
Quo vadis eohippus? The systematics and taxonomy of the early Eocene equids (Perissodactyla)
inferred← citeshttps://doi.org/10.1046/j.1096-3642.2003.00048.xopenalex-snapshot
Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters
inferred← citeshttps://doi.org/10.1046/j.1420-9101.2002.00440.xopenalex-snapshot
Evidence for cryptic hybridization between different evolutionary lineages of the invasive clam genus Corbicula (Veneroida, Bivalvia)
inferred← citeshttps://doi.org/10.1046/j.1463-6409.2003.00133.xopenalex-snapshot
Patterns of septal biomineralization in Scleractinia compared with their 28S rRNA phylogeny: a dual approach for a new taxonomic framework
inferred← citeshttps://doi.org/10.1071/9780643090149.part01openalex-snapshot
General Comparative Biology of the Monocots
inferred← citeshttps://doi.org/10.1073/pnas.0606318104openalex-snapshot
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
inferred← citeshttps://doi.org/10.1073/pnas.96.18.9979openalex-snapshot
SINEs of the perfect character
inferred← citeshttps://doi.org/10.1080/02724634.1999.10011129openalex-snapshot
Phylogenetic systematics of basal perissodactyls
inferred← citeshttps://doi.org/10.1080/09670262.2019.1663269openalex-snapshot
Comparison of colonial volvocine algae based on phylotranscriptomic analysis of gene family evolution and natural selection
inferred← citeshttps://doi.org/10.1080/10409230290771474openalex-snapshot
Utility of Low-Copy Nuclear Gene Sequences in Plant Phylogenetics
inferred← citeshttps://doi.org/10.1080/10635150118268openalex-snapshot
Philosophy and Phylogenetic Inference: A Comparison of Likelihood and Parsimony Methods in the Context of Karl Popper's Writings on Corroboration
inferred← citeshttps://doi.org/10.1080/10635150119012openalex-snapshot
Changing the Landscape: A New Strategy for Estimating Large Phylogenies
inferred← citeshttps://doi.org/10.1080/10635150120230openalex-snapshot
Multiple Molecular Data Sets Suggest Independent Origins of Highly Eusocial Behavior in Bees (Hymenoptera:Apinae)
inferred← citeshttps://doi.org/10.1080/10635150390218330openalex-snapshot
Missing Data, Incomplete Taxa, and Phylogenetic Accuracy
inferred← citeshttps://doi.org/10.1080/10635150490423962openalex-snapshot
Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium
inferred← citeshttps://doi.org/10.1080/10635150500221028openalex-snapshot
How Much Data are Needed to Resolve a Difficult Phylogeny? Case Study in Lamiales
inferred← citeshttps://doi.org/10.1080/10635150500433565openalex-snapshot
Comparative Performance of Bayesian and AIC-Based Measures of Phylogenetic Model Uncertainty
inferred← citeshttps://doi.org/10.1080/10635150500541730openalex-snapshot
Multiple Sequence Alignment Accuracy and Phylogenetic Inference
inferred← citeshttps://doi.org/10.1080/10635150600899798openalex-snapshot
The Effect of Combining Molecular and Morphological Data in Published Phylogenetic Analyses
inferred← citeshttps://doi.org/10.1080/10635150701281102openalex-snapshot
Alignment and Topological Accuracy of the Direct Optimization approach via POY and Traditional Phylogenetics via ClustalW + PAUP*
inferred← citeshttps://doi.org/10.1080/10635150801888871openalex-snapshot
Resolving an Ancient, Rapid Radiation in Saxifragales
inferred← citeshttps://doi.org/10.1080/106351598260572openalex-snapshot
Phylogenetic Congruence and Discordance Among One Morphological and Three Molecular Data Sets from Pontederiaceae
inferred← citeshttps://doi.org/10.1080/106351598260581openalex-snapshot
Combining Data Sets with Different Phylogenetic Histories
inferred← citeshttps://doi.org/10.1080/106351598260680openalex-snapshot
Taxon Sampling and the Accuracy of Large Phylogenies
inferred← citeshttps://doi.org/10.1080/106351598260806openalex-snapshot
Testing Phylogenetic Methods with Tree Congruence: Phylogenetic Analysis of Polymorphic Morphological Characters in Phrynosomatid Lizards
inferred← citeshttps://doi.org/10.1080/106351598260897openalex-snapshot
Phylogenetic Analysis and Intraspecific Variation: Performance of Parsimony, Likelihood, and Distance Methods
inferred← citeshttps://doi.org/10.1080/106351598260923openalex-snapshot
Data Decisiveness, Data Quality, and Incongruence in Phylogenetic Analysis: An Example From the Monocotyledons Using Mitochondrial atp A Sequences
inferred← citeshttps://doi.org/10.1080/106351598261003openalex-snapshot
Sensitivity of Phylogeny Estimation to Taxonomic Sampling
inferred← citeshttps://doi.org/10.1080/106351598261012openalex-snapshot
Inferring Complex Phylogenies Using Parsimony: An Empirical Approach Using Three Large DNA Data Sets for Angiosperms
inferred← citeshttps://doi.org/10.1080/106351598261021openalex-snapshot
Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators
inferred← citeshttps://doi.org/10.1080/14772019.2013.839584openalex-snapshot
Species-level phylogenetic revision of the Ordovician orthide brachiopod Glyptorthis from North America
inferred← citeshttps://doi.org/10.1086/303362openalex-snapshot
Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations
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/bib/bbr014openalex-snapshot
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
inferred← citeshttps://doi.org/10.1093/bioinformatics/12.6.469openalex-snapshot
Bi-De: an application for simulating phylogenetic processes
inferred← citeshttps://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferred← citeshttps://doi.org/10.1093/gbe/evx198openalex-snapshot
Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale
inferred← citeshttps://doi.org/10.1093/jhered/89.4.301openalex-snapshot
Genetic variability in Guadalupe fur seals
inferred← citeshttps://doi.org/10.1093/molbev/msh137openalex-snapshot
Genome-Scale Phylogeny and the Detection of Systematic Biases
inferred← citeshttps://doi.org/10.1093/molbev/msi081openalex-snapshot
Protein Structural Influences in Rhodopsin Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msp105openalex-snapshot
A Machine-Learning Approach Reveals That Alignment Properties Alone Can Accurately Predict Inference of Lateral Gene Transfer from Discordant Phylogenies
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003908openalex-snapshot
Molecular Insights into the Evolution of the Family Bovidae: A Nuclear DNA Perspective
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025595openalex-snapshot
Phylogenetic relationships within the Alcidae (Charadriiformes: Aves) inferred from total molecular evidence
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025619openalex-snapshot
A nuclear gene for higher level phylogenetics: phosphoenolpyruvate carboxykinase tracks mesozoic-age divergences within Lepidoptera (Insecta)
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a025716openalex-snapshot
Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026008openalex-snapshot
The Effect of Taxonomic Sampling on Accuracy of Phylogeny Estimation: Test Case of a Known Phylogeny
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/sysbio/44.1.64openalex-snapshot
Testing Species Phylogenies and Phylogenetic Methods with Congruence
inferred← citeshttps://doi.org/10.1093/sysbio/45.4.393openalex-snapshot
Data Set Incongruence and the Phylogeny of Crocodilians
inferred← citeshttps://doi.org/10.1093/sysbio/46.2.332openalex-snapshot
Accuracy of Phylogenetic Analysis Including and Excluding Polymorphic Characters
inferred← citeshttps://doi.org/10.1093/sysbio/46.3.373openalex-snapshot
Phylogeny of Lichen- and Non-Lichen-Forming Omphalinoid Mushrooms and the Utility of Testing for Combinability among Multiple Data Sets
inferred← citeshttps://doi.org/10.1093/sysbio/46.3.464openalex-snapshot
Is Congruence Between Data Partitions a Reliable Predictor of Phylogenetic Accuracy? Empirically Testing an Iterative Procedure for Choosing Among Phylogenetic Methods
inferred← citeshttps://doi.org/10.1093/sysbio/46.4.622openalex-snapshot
Molecular Systematics of the Canidae
inferred← citeshttps://doi.org/10.1093/sysbio/49.2.306openalex-snapshot
Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences
inferred← citeshttps://doi.org/10.1093/sysbio/syac076openalex-snapshot
Evaluating the Impact of Anatomical Partitioning on Summary Topologies Obtained with Bayesian Phylogenetic Analyses of Morphological Data
inferred← citeshttps://doi.org/10.1093/sysbio/syp056openalex-snapshot
The Use and Validity of Composite Taxa in Phylogenetic Analysis
inferred← citeshttps://doi.org/10.1093/sysbio/syq073openalex-snapshot
The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
inferred← citeshttps://doi.org/10.1093/sysbio/sys072openalex-snapshot
Low-Parameter Phylogenetic Inference Under the General Markov Model
inferred← citeshttps://doi.org/10.1093/sysbio/syv058openalex-snapshot
How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlag085openalex-snapshot
Convergent evolution in the unique and bizarre buccopharyngeal morphology of sand-eating Malagasy tadpoles (Anura: Mantellidae)
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/rsbl.2016.0328openalex-snapshot
Inferring node dates from tip dates in fossil Canidae: the importance of tree priors
inferred← citeshttps://doi.org/10.1098/rspb.1999.0689openalex-snapshot
Molecular phylogenetic evidence for the evolution of specialization in anemonefishes
inferred← citeshttps://doi.org/10.1098/rstb.1998.0353openalex-snapshot
A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters, with an emphasis on the rails (Rallidae)
inferred← citeshttps://doi.org/10.1098/rstb.2005.1735openalex-snapshot
From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction
inferred← citeshttps://doi.org/10.1101/2022.10.21.513246openalex-snapshot
The Genomic Diversity of the Eliurus genus in northern Madagascar with a Putative New Species
inferred← citeshttps://doi.org/10.1109/bibe.2003.1188934openalex-snapshot
A collapsing method for the efficient recovery of optimal edges in phylogenetic trees
inferred← citeshttps://doi.org/10.1109/bmei.2008.247openalex-snapshot
Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks
inferred← citeshttps://doi.org/10.1109/tcbb.2012.62openalex-snapshot
Refining Regulatory Networks through Phylogenetic Transfer of Information
inferred← citeshttps://doi.org/10.1111/bij.12317openalex-snapshot
Molecular and morphological evidence for a Pleistocene radiation of laminate-toothed rats (Otomys: Rodentia) across a volcanic archipelago in equatorial Africa
inferred← citeshttps://doi.org/10.1111/cla.12216openalex-snapshot
Statistical consistency and phylogenetic inference: a brief review
inferred← citeshttps://doi.org/10.1111/ddi.12188openalex-snapshot
Phylogenetic trees do not reliably predict feature diversity
inferred← citeshttps://doi.org/10.1111/ivb.12133openalex-snapshot
Ernst Mayr, causal understanding, and systematics: an example using sabelliform polychaetes
inferred← citeshttps://doi.org/10.1111/j.0014-3820.2000.tb01237.xopenalex-snapshot
MOLECULAR EVOLUTION, ADAPTIVE RADIATION, AND GEOGRAPHIC DIVERSIFICATION IN THE AMPHIATLANTIC FAMILY RAPATEACEAE: EVIDENCE FROM ndhF SEQUENCES AND MORPHOLOGY
inferred← citeshttps://doi.org/10.1111/j.1095-8312.2008.01153.xopenalex-snapshot
Speciation mirrors geomorphology and palaeoclimatic history in African laminate-toothed rats (Muridae: Otomyini) of the Otomys denti and Otomys lacustris species-complexes in the ‘Montane Circle’ of East Africa
inferred← citeshttps://doi.org/10.1111/j.1096-0031.1995.tb00002.xopenalex-snapshot
NOTHOFAGUSAND PACIFIC BIOGEOGRAPHY
inferred← citeshttps://doi.org/10.1111/j.1096-0031.1996.tb00194.xopenalex-snapshot
ON CONSENSUS, CONFIDENCE, AND “TOTAL EVIDENCE”
inferred← citeshttps://doi.org/10.1111/j.1096-0031.1997.tb00322.xopenalex-snapshot
Probabilism and Phylogenetic Inference
inferred← citeshttps://doi.org/10.1111/j.1096-0031.1998.tb00328.xopenalex-snapshot
Total Evidence Or Taxonomic Congruence: Cladistics Or Consensus Classification
inferred← citeshttps://doi.org/10.1111/j.1096-0031.1999.tb00391.xopenalex-snapshot
Long-Branch Abstractions
inferred← citeshttps://doi.org/10.1111/j.1096-0031.2002.tb00142.xopenalex-snapshot
Testing Methods: The Evaluation of Discovery Operations in Evolutionary Biology
inferred← citeshttps://doi.org/10.1111/j.1096-0031.2003.tb00311.xopenalex-snapshot
Data exploration in phylogenetic inference: scientific, heuristic, or neither
inferred← citeshttps://doi.org/10.1111/j.1096-0031.2008.00213.xopenalex-snapshot
Finding an upper limit for gap costs in direct optimization parsimony
inferred← citeshttps://doi.org/10.1111/j.1096-3642.1997.tb01285.xopenalex-snapshot
A phylogenetic analysis of basal Anseriformes, the fossil Presbyornis, and the interordinal relationships of waterfowl
inferred← citeshttps://doi.org/10.1111/j.1096-3642.2010.00619.xopenalex-snapshot
Delimiting baridine weevil evolution (Coleoptera: Curculionidae: Baridinae)
inferred← citeshttps://doi.org/10.1111/j.1365-2915.2009.00828.xopenalex-snapshot
A host species‐informative internal control for molecular assessment of African swine fever virus infection rates in the African sylvatic cycle Ornithodoros vector
inferred← citeshttps://doi.org/10.1111/j.1462-2920.2005.00929.xopenalex-snapshot
Bacterial diversity in the rhizosphere of Proteaceae species
inferred← citeshttps://doi.org/10.1111/j.1463-6409.2005.00168.xopenalex-snapshot
Total evidence requires exclusion of phylogenetically misleading data
inferred← citeshttps://doi.org/10.1111/j.1463-6409.2006.00277.xopenalex-snapshot
A falsificationist perspective on the usage of process frequencies in phylogenetics
inferred← citeshttps://doi.org/10.1111/j.1463-6409.2009.00413.xopenalex-snapshot
Recovering phylogenetic signal from frog mating calls
inferred← citeshttps://doi.org/10.1111/j.1469-7998.2008.00542.xopenalex-snapshot
When is a species not a species? Uncoupled phenotypic, karyotypic and genotypic divergence in two species of South African laminate‐toothed rats (Murinae: Otomyini)
inferred← citeshttps://doi.org/10.1111/j.1558-5646.1996.tb04467.xopenalex-snapshot
PERSPECTIVE: EVOLUTIONARY PATTERNS IN THE FOSSIL RECORD
inferred← citeshttps://doi.org/10.1146/annurev.ecolsys.30.1.327openalex-snapshot
Polymorphism in Systematics and Comparative Biology
inferred← citeshttps://doi.org/10.11606/t.42.2001.tde-01112001-123050openalex-snapshot
Caracterização e filogenia moleculares de Acanthamoeba.
inferred← citeshttps://doi.org/10.1162/106454604773563540openalex-snapshot
Experiments in Digital Evolution (Editors' Introduction to the Special Issue)
inferred← citeshttps://doi.org/10.1162/106454604773563586openalex-snapshot
Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods
inferred← citeshttps://doi.org/10.11646/phytotaxa.1.1.2openalex-snapshot
Phylogenetic analysis of non-coding plastid DNA in the presence of short inversions
inferred← citeshttps://doi.org/10.1177/117693430500100007openalex-snapshot
MySSP: Non-stationary evolutionary sequence simulation, including indels
inferred← citeshttps://doi.org/10.1186/1471-2105-12-184openalex-snapshot
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation
inferred← citeshttps://doi.org/10.1186/1471-2148-7-94openalex-snapshot
The effect of natural selection on the performance of maximum parsimony
inferred← citeshttps://doi.org/10.1186/1745-6150-1-5openalex-snapshot
Phylogenetic inference from homologous sequence data: minimum topological assumption, strict mutational compatibility consensus tree as the ultimate solution.
inferred← citeshttps://doi.org/10.1186/1748-7188-5-1openalex-snapshot
Refining transcriptional regulatory networks using network evolutionary models and gene histories
inferred← citeshttps://doi.org/10.1201/b18597-10openalex-snapshot
Molecular Phylogenetics: A Tool for Elucidation of Evolutionary Processes from Biological Data
inferred← citeshttps://doi.org/10.1214/lnms/1215455553openalex-snapshot
Uses of statistical parsimony in HIV analyses
inferred← citeshttps://doi.org/10.1371/journal.pone.0001913openalex-snapshot
A Comparison of Phylogenetic Network Methods Using Computer Simulation
inferred← citeshttps://doi.org/10.1371/journal.pone.0042925openalex-snapshot
Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling
inferred← citeshttps://doi.org/10.1371/journal.pone.0101341openalex-snapshot
Secondary Structure Analyses of the Nuclear rRNA Internal Transcribed Spacers and Assessment of Its Phylogenetic Utility across the Brassicaceae (Mustards)
inferred← citeshttps://doi.org/10.1371/journal.pone.0123894openalex-snapshot
Mitochondrial DNA Genomes Organization and Phylogenetic Relationships Analysis of Eight Anemonefishes (Pomacentridae: Amphiprioninae)
inferred← citeshttps://doi.org/10.1525/9780520944473-022openalex-snapshot
21. A CRITIQUE OF EXPERIMENTAL PHYLOGENETICS
inferred← citeshttps://doi.org/10.1525/california/9780520247666.001.0001openalex-snapshot
Experimental EvolutionConcepts, Methods, and Applications of Selection Experiments
inferred← citeshttps://doi.org/10.1534/genetics.107.081018openalex-snapshot
Phylogenetic Fate Mapping: Theoretical and Experimental Studies Applied to the Development of Mouse Fibroblasts
inferred← citeshttps://doi.org/10.1575/1912/5574openalex-snapshot
Evolutionary patterns within the Anthozoa (phylum Cindaria) reflected in ribosomal gene sequences
inferred← citeshttps://doi.org/10.1600/0363644054223530openalex-snapshot
Molecular Markers Reject Monophyly of the Subgenera of Satyrium (Orchidaceae)
inferred← citeshttps://doi.org/10.1600/036364406775971769openalex-snapshot
Phylogenetic Relationships and Chromosome Number Evolution in Passiflora
inferred← citeshttps://doi.org/10.1600/036364406777585739openalex-snapshot
Coding Quantitative Character Data for Phylogenetic Analysis: A Comparison of Five Methods
inferred← citeshttps://doi.org/10.1666/0022-3360(2003)077<0189:rshtaa>2.0.co;2openalex-snapshot
RESOLUTION, SAMPLING, HIGHER TAXA AND ASSUMPTIONS IN STRATOCLADISTIC ANALYSIS
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