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Models of Molecular Evolution and Phylogeny: Table 1.
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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/jmbi.1996.0569openalex-snapshot
Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses
inferredcites →https://doi.org/10.1006/mpev.1994.1026openalex-snapshot
A Stochastic Model for the Evolution of Autocorrelated DNA Sequences
inferredcites →https://doi.org/10.1007/978-1-4612-1694-0_15openalex-snapshot
Information Theory and an Extension of the Maximum Likelihood Principle
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/bf00160155openalex-snapshot
Estimation of evolutionary distances between nucleotide sequences
inferredcites →https://doi.org/10.1007/bf00162968openalex-snapshot
The influence of nearest neighbors on the rate and pattern of spontaneous point mutations
inferredcites →https://doi.org/10.1007/bf00163848openalex-snapshot
Inching toward reality: An improved likelihood model of sequence evolution
inferredcites →https://doi.org/10.1007/bf00166252openalex-snapshot
Statistical tests of models of DNA substitution
inferredcites →https://doi.org/10.1007/bf00173195openalex-snapshot
Tree-based maximal likelihood substitution matrices and hidden Markov models
inferredcites →https://doi.org/10.1007/bf00173421openalex-snapshot
Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
inferredcites →https://doi.org/10.1007/bf00178256openalex-snapshot
Estimating the pattern of nucleotide substitution
inferredcites →https://doi.org/10.1007/bf00182387openalex-snapshot
Directional mutation pressure, selective constraints, and genetic equilibria
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/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/bf01840889openalex-snapshot
Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide
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/bf02101990openalex-snapshot
A new method for calculating evolutionary substitution rates
inferredcites →https://doi.org/10.1007/bf02105807openalex-snapshot
A method of estimating from two aligned present-day DNA sequences their ancestral composition and subsequent rates of substitution, possibly different in the two lineages, corrected for multiple and parallel substitutions at the same site
inferredcites →https://doi.org/10.1007/bf02109483openalex-snapshot
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
inferredcites →https://doi.org/10.1007/bf02193625openalex-snapshot
An evolutionary model for maximum likelihood alignment of DNA sequences
inferredcites →https://doi.org/10.1007/bf02198856openalex-snapshot
Phylogenetic analysis using parsimony and likelihood methods
inferredcites →https://doi.org/10.1007/bf02352289openalex-snapshot
Maximum-likelihood models for combined analyses of multiple sequence data
inferredcites →https://doi.org/10.1007/bf02458837openalex-snapshot
Stochastic models for heterogeneous DNA sequences
inferredcites →https://doi.org/10.1007/bf02498640openalex-snapshot
Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA
inferredcites →https://doi.org/10.1007/pl00006274openalex-snapshot
Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences
inferredcites →https://doi.org/10.1007/pl00006320openalex-snapshot
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
inferredcites →https://doi.org/10.1016/0014-5793(94)80429-xopenalex-snapshot
A mutation data matrix for transmembrane proteins
inferredcites →https://doi.org/10.1016/0169-5347(96)10041-0openalex-snapshot
Among-site rate variation and its impact on phylogenetic analyses
inferredcites →https://doi.org/10.1016/b978-1-4832-2734-4.50017-6openalex-snapshot
Evolutionary Divergence and Convergence in Proteins
inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot
Evolution of Protein Molecules
inferredcites →https://doi.org/10.1016/s0022-5193(05)80092-xopenalex-snapshot
Mammalian DNA replication: Mutation biases and the mutation rate
inferredcites →https://doi.org/10.1038/41460openalex-snapshot
Structural biology and phylogenetic estimation
inferredcites →https://doi.org/10.1063/1.3034322openalex-snapshot
An Introduction to Probability Theory and Its Applications, Vol. 2
inferredcites →https://doi.org/10.1073/pnas.79.10.3246openalex-snapshot
Novel features of animal mtDNA evolution as shown by sequences of two rat cytochrome oxidase subunit II genes.
inferredcites →https://doi.org/10.1073/pnas.85.24.9630openalex-snapshot
Universal rule for coding sequence construction: TA/CG deficiency-TG/CT excess.
inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot
Amino acid substitution matrices from protein blocks.
inferredcites →https://doi.org/10.1080/106351598260996openalex-snapshot
Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?
inferredcites →https://doi.org/10.1080/106351598261067openalex-snapshot
On the Best Evolutionary Rate for Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/14.8.726openalex-snapshot
PASSML: combining evolutionary inference and protein secondary structure prediction.
inferredcites →https://doi.org/10.1093/bioinformatics/8.3.275openalex-snapshot
The rapid generation of mutation data matrices from protein sequences
inferredcites →https://doi.org/10.1093/genetics/134.2.597openalex-snapshot
Rates and patterns of base change in the small subunit ribosomal RNA gene.
inferredcites →https://doi.org/10.1093/genetics/139.2.993openalex-snapshot
A space-time process model for the evolution of DNA sequences.
inferredcites →https://doi.org/10.1093/genetics/141.2.771openalex-snapshot
Estimating substitution rates in ribosomal RNA genes.
inferredcites →https://doi.org/10.1093/genetics/148.4.1993openalex-snapshot
High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA
inferredcites →https://doi.org/10.1093/genetics/149.1.445openalex-snapshot
Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
inferredcites →https://doi.org/10.1093/genetics/98.3.641openalex-snapshot
A MODEL OF EVOLUTIONARY BASE SUBSTITUTIONS AND ITS APPLICATION WITH SPECIAL REFERENCE TO RAPID CHANGE OF PSEUDOGENES
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025575openalex-snapshot
A Hidden Markov Model approach to variation among sites in rate of evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025627openalex-snapshot
Combining protein evolution and secondary structure
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025664openalex-snapshot
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025811openalex-snapshot
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026006openalex-snapshot
A codon-based model designed to describe lentiviral evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040023openalex-snapshot
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
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.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.a040261openalex-snapshot
The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040410openalex-snapshot
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040633openalex-snapshot
Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants.
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.1994.0006openalex-snapshot
Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters
inferredcites →https://doi.org/10.1098/rspb.1998.0502openalex-snapshot
Phylogenetic information and experimental design in molecular systematics
inferredcites →https://doi.org/10.1109/5.18626openalex-snapshot
A tutorial on hidden Markov models and selected applications in speech recognition
inferredcites →https://doi.org/10.1111/j.0006-341x.1999.00001.xopenalex-snapshot
Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
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.1558-5646.1997.tb01461.xopenalex-snapshot
CORRELATED RATES OF MOLECULAR AND MORPHOLOGICAL EVOLUTION
inferredcites →https://doi.org/10.1126/science.1439790openalex-snapshot
Ikaros, an Early Lymphoid-Specific Transcription Factor and a Putative Mediator for T Cell Commitment
inferredcites →https://doi.org/10.1126/science.147.3653.68openalex-snapshot
Evolving Genes and Proteins
inferredcites →https://doi.org/10.1126/science.1604319openalex-snapshot
Exhaustive Matching of the Entire Protein Sequence Database
inferredcites →https://doi.org/10.1126/science.185.4154.862openalex-snapshot
Amino Acid Difference Formula to Help Explain Protein Evolution
inferredcites →https://doi.org/10.1126/science.2683084openalex-snapshot
Chromosomal Location and Evolutionary Rate Variation in Enterobacterial Genes
inferredcites →https://doi.org/10.1126/science.276.5310.227openalex-snapshot
Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context
inferredcites →https://doi.org/10.1126/science.8342022openalex-snapshot
Greater Susceptibility to Mutations in Lagging Strand of DNA Replication in Escherichia coli than in Leading Strand
inferredcites →https://doi.org/10.2307/2412304openalex-snapshot
Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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How complex is the Naineris setosa species complex? First integrative study of a presumed cosmopolitan and invasive annelid (Sedentaria: Orbiniidae)
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Adaptive Molecular Evolution
inferred← citeshttps://doi.org/10.1002/9780470061619.ch14openalex-snapshot
Probabilistic Models for the Study of Protein Evolution
inferred← citeshttps://doi.org/10.1002/9780471650126.dob0515.pub2openalex-snapshot
PAML (Phylogenetic Analysis by Maximum Likelihood)
inferred← citeshttps://doi.org/10.1002/9781119162254.ch03openalex-snapshot
Sampling Techniques: Estimating Evolutionary Rates and Generating Molecular Structures
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Identification of protein functional surfaces by the concept of a split pocket
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Evolutionary model of protein secondary structure capable of revealing new biological relationships
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Phylogenetic Hidden Markov Models
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Estimating Substitution Matrices
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Molecular Phylogenetics: Concepts for a Newcomer
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Using Multiple Alignments to Improve Gene Prediction
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Sequence Learning via Bayesian Clustering by Dynamics
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A Chemical-Distance-Based Test for Positive Darwinian Selection
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Phylogenetic Methods for Genome-Wide Association Studies in Bacteria
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Methodologies for Microbial Ancestral Sequence Reconstruction
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Molecular Phylogenetics: Testing Evolutionary Hypotheses
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When THAT Rule Almost Persists as THAT Rule
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Genome Analysis of Plants
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The Structurally Constrained Neutral Model of Protein Evolution
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Bayesian Phylogeny on Grid
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Computing Substitution Matrices for Genomic Comparative Analysis
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Irreplaceable Amino Acids and Reduced Alphabets in Short-Term and Directed Protein Evolution
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Back-Translation for Discovering Distant Protein Homologies
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Substitution Matrices and Mutual Information Approaches to Modeling Evolution
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Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA
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Molecular Evolution of Parasitic Helminths
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Modeling Mitochondrial Protein Evolution Using Structural Information
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Are Radical and Conservative Substitution Rates Useful Statistics in Molecular Evolution?
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Modeling DNA Base Substitution in Large Genomic Regions from Two Organisms
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Assessing Substitution Variation Across Sites in Grass Chloroplast DNA
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The Effect of Branch Length Variation on the Selection of Models of Molecular Evolution
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Niche partitioning and phylogenetic distance of rotifer species revealed by the four-year temporal dynamics in a small mountain lake
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Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions
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Learning epistatic interactions from sequence-activity data to predict enantioselectivity
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Genetic characterization and pathogenicity assessment of Newcastle disease virus isolated from wild peacock
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Identifiability and Reconstructibility of Species Phylogenies Under a Modified Coalescent
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Savoronala, a new genus of Malmideaceae (Lecanorales) from Madagascar with stipes producing sporodochia
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Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution
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Tutorial on phylogenetic inference — 2
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Comparison of DNA extraction methods for non-marine molluscs: is modified CTAB DNA extraction method more efficient than DNA extraction kits?
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Molecular data resolve a new order of Arthoniomycetes sister to the primarily lichenized Arthoniales and composed of black yeasts, lichenicolous and rock-inhabiting species
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Diversity, ecology and molecular phylogeny of genus Litsea (Lauraceae) in Central Western Ghat areas of India
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Phylogenetic Character Reconstruction
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Phylogenetic Character Reconstruction
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Stability and numerical simulation of a fractional order plant-nectar-pollinator model
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A quartet-based approach for inferring phylogenetically informative features from genomic and phenomic data
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Molecular phylogeny of genus Nothopegia Blume nom.cons. (Anacardiaceae) in Central Western Ghats Karnataka, based on the ITS, rbcL and trnLF markers
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Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles
inferred← citeshttps://doi.org/10.1016/j.gene.2006.11.022openalex-snapshot
Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny
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Evolution of protein families: Is it possible to distinguish between domains of life?
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Resolving network clusters disparity based on dissimilarity measurements with nonmetric analysis of variance
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Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
inferred← citeshttps://doi.org/10.1016/j.jmb.2003.11.007openalex-snapshot
Are Residues in a Protein Folding Nucleus Evolutionarily Conserved?
inferred← citeshttps://doi.org/10.1016/j.jmb.2011.06.005openalex-snapshot
Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models
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A new criterion and method for amino acid classification
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Towards optimal distance functions for stochastic substitution models
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Identifiability of speciation times under the multispecies coalescent
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Trajectory analysis for user verification and recognition
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Context-dependent substitution models for circular DNA
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High concentration of basidiolichens in a single family of agaricoid mushrooms (Basidiomycota: Agaricales: Hygrophoraceae)
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Codon information value and codon transition-probability distributions in short-term evolution
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Eigen’s paradox and the quasispecies model in a non-Archimedean framework
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DNA sequencing reveals false positives during the detection of aster yellows phytoplasmas in leafhoppers
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Large-scale sequencing and the new animal phylogeny
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Cloning and analysis of the lamprey GnRH-III cDNA from eight species of lamprey representing the three families of Petromyzoniformes
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Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota)
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Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene
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BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction
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MtPAN3: Site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola
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A road map for phylogenetic models of species trees
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Molecular phylogenetics: state-of-the-art methods for looking into the past
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Detecting excess radical replacements in phylogenetic trees
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Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates
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KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging
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Methods for Computational Gene Prediction
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Selecting models of evolution
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Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences
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Bayesian Clustering by Dynamics
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Genomic Characterization of a Slow/Low Maedi Visna Virus
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Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing
inferred← citeshttps://doi.org/10.1038/nature03222openalex-snapshot
Detecting selection needs comparative data
inferred← citeshttps://doi.org/10.1038/npg.els.0006039openalex-snapshot
Proteins: Mutational Effects in
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A biologist’s guide to Bayesian phylogenetic analysis
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Assessing phylogenetic confidence at pandemic scales
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Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s
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/10.1073/pnas.1906020116openalex-snapshot
Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination
inferred← citeshttps://doi.org/10.1080/10635150119988openalex-snapshot
A Partitioned Likelihood Analysis of Swallowtail Butterfly Phylogeny (Lepidoptera: Papilionidae)
inferred← citeshttps://doi.org/10.1080/10635150500354688openalex-snapshot
An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction
inferred← citeshttps://doi.org/10.1088/1751-8121/aaebb1openalex-snapshot
Non-Archimedean replicator dynamics and Eigen’s paradox
inferred← citeshttps://doi.org/10.1089/1066527041410472openalex-snapshot
Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis
inferred← citeshttps://doi.org/10.1089/cmb.2006.13.379openalex-snapshot
Using Multiple Alignments to Improve Gene Prediction
inferred← citeshttps://doi.org/10.1089/cmb.2009.0236openalex-snapshot
Adaptive Distance Measures for Resolving K2P Quartets: Metric Separation versus Stochastic Noise
inferred← citeshttps://doi.org/10.1093/bib/bbm051openalex-snapshot
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
inferred← citeshttps://doi.org/10.1093/bib/bbn049openalex-snapshot
Models of coding sequence evolution
inferred← citeshttps://doi.org/10.1093/bioinformatics/17.7.662openalex-snapshot
PAL: an object-oriented programming library for molecular evolution and phylogenetics
inferred← citeshttps://doi.org/10.1093/bioinformatics/19.2.219openalex-snapshot
Gene finding with a hidden Markov model of genome structure and evolution
inferred← citeshttps://doi.org/10.1093/bioinformatics/bth105openalex-snapshot
Regional and time-resolved mutation patterns of the human genome
inferred← citeshttps://doi.org/10.1093/bioinformatics/bth942openalex-snapshot
Improved techniques for the identification of pseudogenes
inferred← citeshttps://doi.org/10.1093/bioinformatics/bti376openalex-snapshot
Identification and measurement of neighbor-dependent nucleotide substitution processes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btk001openalex-snapshot
A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm024openalex-snapshot
A simulation test bed for hypotheses of genome evolution
inferred← citeshttps://doi.org/10.1093/bioinformatics/btn391openalex-snapshot
Is there an acceleration of the CpG transition rate during the mammalian radiation?
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt530openalex-snapshot
Protein evolution along phylogenetic histories under structurally constrained substitution models
inferred← citeshttps://doi.org/10.1093/gbe/evr032openalex-snapshot
Faster than Neutral Evolution of Constrained Sequences: The Complex Interplay of Mutational Biases and Weak Selection
inferred← citeshttps://doi.org/10.1093/gbe/evs110openalex-snapshot
Mutational Dynamics of Aroid Chloroplast Genomes
inferred← citeshttps://doi.org/10.1093/gbe/evu223openalex-snapshot
The Influence of Selection for Protein Stability on dN/dS Estimations
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/gbe/evw308openalex-snapshot
Standard Codon Substitution Models Overestimate Purifying Selection for Non-Stationary Data
inferred← citeshttps://doi.org/10.1093/genetics/155.1.431openalex-snapshot
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
inferred← citeshttps://doi.org/10.1093/genetics/159.1.347openalex-snapshot
Selection at the Amino Acid Level Can Influence Synonymous Codon Usage: Implications for the Study of Codon Adaptation in Plastid Genes
inferred← citeshttps://doi.org/10.1093/genetics/162.4.1811openalex-snapshot
Likelihood and Bayes Estimation of Ancestral Population Sizes in Hominoids Using Data From Multiple Loci
inferred← citeshttps://doi.org/10.1093/icb/43.4.500openalex-snapshot
Ancestral Gene Reconstruction and Synthesis of Ancient Rhodopsins in the Laboratory
inferred← citeshttps://doi.org/10.1093/molbev/msaa193openalex-snapshot
Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies
inferred← citeshttps://doi.org/10.1093/molbev/msaf124openalex-snapshot
A General Substitution Matrix for Structural Phylogenetics
inferred← citeshttps://doi.org/10.1093/molbev/msh039openalex-snapshot
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood
inferred← citeshttps://doi.org/10.1093/molbev/msh199openalex-snapshot
An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure
inferred← citeshttps://doi.org/10.1093/molbev/msi005openalex-snapshot
Different Versions of the Dayhoff Rate Matrix
inferred← citeshttps://doi.org/10.1093/molbev/msi048openalex-snapshot
Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences
inferred← citeshttps://doi.org/10.1093/molbev/msi076openalex-snapshot
Covarion Structure in Plastid Genome Evolution: A New Statistical Test
inferred← citeshttps://doi.org/10.1093/molbev/msi250openalex-snapshot
A Bayesian Model Comparison Approach to Inferring Positive Selection
inferred← citeshttps://doi.org/10.1093/molbev/msj026openalex-snapshot
Apparent Trends of Amino Acid Gain and Loss in Protein Evolution Due to Nearly Neutral Variation
inferred← citeshttps://doi.org/10.1093/molbev/msj044openalex-snapshot
An Evolutionary Space-Time Model with Varying Among-Site Dependencies
inferred← citeshttps://doi.org/10.1093/molbev/msj048openalex-snapshot
Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach
inferred← citeshttps://doi.org/10.1093/molbev/msl170openalex-snapshot
Bayesian Estimation of Concordance among Gene Trees
inferred← citeshttps://doi.org/10.1093/molbev/msm064openalex-snapshot
An Empirical Codon Model for Protein Sequence Evolution
inferred← citeshttps://doi.org/10.1093/molbev/msn098openalex-snapshot
Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites
inferred← citeshttps://doi.org/10.1093/molbev/msn169openalex-snapshot
Quantifying the Stationarity and Time Reversibility of the Nucleotide Substitution Process
inferred← citeshttps://doi.org/10.1093/molbev/msn286openalex-snapshot
Inferring Selection on Amino Acid Preference in Protein Domains
inferred← citeshttps://doi.org/10.1093/molbev/msp003openalex-snapshot
Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences
inferred← citeshttps://doi.org/10.1093/molbev/msp163openalex-snapshot
Peeling the Onion: Ribosomes Are Ancient Molecular Fossils
inferred← citeshttps://doi.org/10.1093/molbev/msp232openalex-snapshot
Estimates of the Effect of Natural Selection on Protein-Coding Content
inferred← citeshttps://doi.org/10.1093/molbev/msp277openalex-snapshot
Comparing Models of Evolution for Ordered and Disordered Proteins
inferred← citeshttps://doi.org/10.1093/molbev/msr279openalex-snapshot
The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome
inferred← citeshttps://doi.org/10.1093/molbev/msu196openalex-snapshot
A Generalized Mechanistic Codon Model
inferred← citeshttps://doi.org/10.1093/molbev/msw019openalex-snapshot
Robust Estimation of Evolutionary Distances with Information Theory
inferred← citeshttps://doi.org/10.1093/molbev/msz122openalex-snapshot
Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States
inferred← citeshttps://doi.org/10.1093/nar/gkae382openalex-snapshot
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation
inferred← citeshttps://doi.org/10.1093/nar/gkaf1040openalex-snapshot
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
inferred← citeshttps://doi.org/10.1093/nar/gky783openalex-snapshot
Bayesian inference of ancestral dates on bacterial phylogenetic trees
inferred← citeshttps://doi.org/10.1093/nargab/lqaa041openalex-snapshot
A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003851openalex-snapshot
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003857openalex-snapshot
Structural Constraints and Emergence of Sequence Patterns in Protein Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003890openalex-snapshot
Selecting Models of Nucleotide Substitution: An Application to Human Immunodeficiency Virus 1 (HIV-1)
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a003945openalex-snapshot
Accuracy and Power of the Likelihood Ratio Test in Detecting Adaptive Molecular Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004007openalex-snapshot
A Novel Use of Equilibrium Frequencies in Models of Sequence Evolution
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a004089openalex-snapshot
Site-Specific Amino Acid Replacement Matrices from Structurally Constrained Protein Evolution Simulations
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026083openalex-snapshot
Using protein structural information in evolutionary inference: transmembrane proteins
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026219openalex-snapshot
Distributions of Statistics Used for the Comparison of Models of Sequence Evolution in Phylogenetics
inferred← citeshttps://doi.org/10.1093/oxfordjournals.molbev.a026367openalex-snapshot
Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models
inferred← citeshttps://doi.org/10.1093/sysbio/syaa039openalex-snapshot
Consistency of SVDQuartets and Maximum Likelihood for Coalescent-Based Species Tree Estimation
inferred← citeshttps://doi.org/10.1093/sysbio/syab009openalex-snapshot
Of Traits and Trees: Probabilistic Distances under Continuous Trait Models for Dissecting the Interplay among Phylogeny, Model, and Data
inferred← citeshttps://doi.org/10.1093/sysbio/sys024openalex-snapshot
Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context
inferred← citeshttps://doi.org/10.1094/phyto-12-11-0342openalex-snapshot
Diversity Among Ralstonia solanacearum Strains Isolated from the Southeastern United States
inferred← citeshttps://doi.org/10.1098/rsif.2014.1010openalex-snapshot
Evolution on neutral networks accelerates the ticking rate of the molecular clock
inferred← citeshttps://doi.org/10.1098/rsta.2016.0352openalex-snapshot
Resurrecting ancestral genes in bacteria to interpret ancient biosignatures
inferred← citeshttps://doi.org/10.1099/ijsem.0.001280openalex-snapshot
Streptococcus dentiloxodontae sp. nov., isolated from the oral cavity of elephants
inferred← citeshttps://doi.org/10.1101/195669openalex-snapshot
Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes
inferred← citeshttps://doi.org/10.1101/2020.09.24.278218openalex-snapshot
The 4R Genome Duplication In Salmonine Fishes: Insights From Conserved Non-Coding Elements
inferred← citeshttps://doi.org/10.1101/2021.11.19.469283openalex-snapshot
Nonmetric ANOVA: a generic framework for analysis of variance on dissimilarity measures
inferred← citeshttps://doi.org/10.1101/2022.02.27.481992openalex-snapshot
Reconstructing the evolutionary history of a B cell lineage with minimum spanning tree and genotype abundances
inferred← citeshttps://doi.org/10.1101/400465openalex-snapshot
Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers
inferred← citeshttps://doi.org/10.1101/gr.1252603openalex-snapshot
Asymmetric Sequence Divergence of Duplicate Genes
inferred← citeshttps://doi.org/10.1101/gr.844103openalex-snapshot
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
inferred← citeshttps://doi.org/10.1109/eeeic/icpseurope54979.2022.9854737openalex-snapshot
Feature Based Wind Resource Clustering using an Adapted Phylogenetic Gene Sequencing Approach
inferred← citeshttps://doi.org/10.1109/embc.2015.7320293openalex-snapshot
Novel protein weight matrix generated from amino acid indices
inferred← citeshttps://doi.org/10.1109/icbbe.2008.9openalex-snapshot
A Simple Di-Nucleotide Based DNA Analysis Applied to Phylogeny of Mammals using Zinc Fingers
inferred← citeshttps://doi.org/10.1109/iccitechn.2014.7073138openalex-snapshot
An optimized algorithm to find maximum parsimonious tree using PrimeNucleotide based approach
inferred← citeshttps://doi.org/10.1109/iembs.2005.1616520openalex-snapshot
Estimating evolutionary rate of local protein binding surfaces: a Bayesian Monte Carlo approach
inferred← citeshttps://doi.org/10.1109/iembs.2007.4353538openalex-snapshot
Detecting Positively Selected Sites From Amino Acid Sequences: An Implicit Codon Model
inferred← citeshttps://doi.org/10.1111/1574-6968.12207openalex-snapshot
Testing evolutionary models to explain the process of nucleotide substitution in gut bacterial 16S rRNA gene sequences
inferred← citeshttps://doi.org/10.1111/j.1759-6831.2012.00197.xopenalex-snapshot
Caryophyllales: Evaluating phylogenetic signal in trnK intron versus matK
inferred← citeshttps://doi.org/10.1111/jbi.13120openalex-snapshot
Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics
inferred← citeshttps://doi.org/10.1111/jse.12585openalex-snapshot
Correlations among oligonucleotide repeats, nucleotide substitutions, and insertion–deletion mutations in chloroplast genomes of plant family Malvaceae
inferred← citeshttps://doi.org/10.1128/9781555815882.ch90openalex-snapshot
Characterization of Microeukaryota in Natural Environments
inferred← citeshttps://doi.org/10.1128/cvi.00107-16openalex-snapshot
Human Survivors of Disease Outbreaks Caused by Ebola or Marburg Virus Exhibit Cross-Reactive and Long-Lived Antibody Responses
inferred← citeshttps://doi.org/10.1139/cjz-2018-0118openalex-snapshot
Found, forgotten, and found again: systematics and distribution of Cooper’s Rocky Mountain snail (Oreohelix cooperi) on a sky island in the Canadian Prairies
inferred← citeshttps://doi.org/10.1142/9789814447362_0022openalex-snapshot
A MODEL FOR PHYLOGENETIC INFERENCE USING STRUCTURAL AND CHEMICAL COVARIATES
inferred← citeshttps://doi.org/10.1145/640075.640111openalex-snapshot
Combining phylogenetic and hidden Markov models in biosequence analysis
inferred← citeshttps://doi.org/10.1145/974614.974638openalex-snapshot
Computational identification of evolutionarily conserved exons
inferred← citeshttps://doi.org/10.1155/2008/683509openalex-snapshot
Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods
inferred← citeshttps://doi.org/10.1155/2014/434257openalex-snapshot
Molecular Characterization and Screening for Sheath Blight Resistance Using Malaysian Isolates ofRhizoctonia solani
inferred← citeshttps://doi.org/10.11606/t.42.2001.tde-01112001-123050openalex-snapshot
Caracterização e filogenia moleculares de Acanthamoeba.
inferred← citeshttps://doi.org/10.1177/117693430500100004openalex-snapshot
Evolution of Proteins and Proteomes: A Phylogenetics Approach
inferred← citeshttps://doi.org/10.1177/1176934318764683openalex-snapshot
Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes
inferred← citeshttps://doi.org/10.1177/1176934319892284openalex-snapshot
Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review
inferred← citeshttps://doi.org/10.1186/1471-2105-12-18openalex-snapshot
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states
inferred← citeshttps://doi.org/10.1186/1471-2105-12-248openalex-snapshot
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
inferred← citeshttps://doi.org/10.1186/1471-2105-5-1openalex-snapshot
PyEvolve: a toolkit for statistical modelling of molecular evolution
inferred← citeshttps://doi.org/10.1186/1471-2105-6-130openalex-snapshot
Vestige: Maximum likelihood phylogenetic footprinting
inferred← citeshttps://doi.org/10.1186/1471-2105-7-476openalex-snapshot
Using the nucleotide substitution rate matrix to detect horizontal gene transfer
inferred← citeshttps://doi.org/10.1186/1471-2105-9-511openalex-snapshot
Comparison of methods for estimating the nucleotide substitution matrix
inferred← citeshttps://doi.org/10.1186/1471-2105-9-550openalex-snapshot
Pathological rate matrices: from primates to pathogens
inferred← citeshttps://doi.org/10.1186/1471-2148-6-44openalex-snapshot
Computing Ka and Ks with a consideration of unequal transitional substitutions
inferred← citeshttps://doi.org/10.1186/1471-2164-14-750openalex-snapshot
Heterogeneity in the entire genome for three genotypes of peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants
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