Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
1994/09/01 by Ziheng Yang · 99 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Genomics and Phylogenetic Studies #Evolution and Paleontology Studies #Genetic diversity and population structure
paper · doi:10.1007/bf00160154
Citations
Cited by
- Phylogenetic position and revised classification of<i>Acacia s.l.</i>(Fabaceae: Mimosoideae) in Africa, including new combinations in<i>Vachellia</i>and<i>Senegalia</i>
- The origin of a mega-diverse genus: dating<i>Begonia</i>(Begoniaceae) using alternative datasets, calibrations and relaxed clock methods
- Molecular phylogeny and historical biogeography of the large carpenter bees, genus Xylocopa (Hymenoptera: Apidae)
- Ancient genomes reveal a deep history of Treponema pallidum in the Americas
- Earliest short-tailed bird from the Late Jurassic of China
- Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity
- A global phylogeny of grammitid ferns (Polypodiaceae) and its systematic implications
- Evolutionary Relations of Hexanchiformes Deep-Sea Sharks Elucidated by Whole Mitochondrial Genome Sequences
- Around the World in 26 Million Years: Diversification and Biogeography of Pantropical Grass‐Yellow <i>Eurema</i> Butterflies (Pieridae: Coliadinae)
- Tempo and mode of winter diapause evolution in butterflies
- The evolutionary relationships and age of Homo naledi: An assessment using dated Bayesian phylogenetic methods
- PHYLOGENETIC ANALYSIS IN MOLECULAR EVOLUTIONARY GENETICS
- IQ-TREE 3: phylogenomic inference software using complex evolutionary models
- Identification of a distinct family of polyphosphate kinases relevant to energy homeostasis in Crenarchaeota
- Phylogeny of Athyridida (Brachiopoda): a comparison of methods of inference
- Reduced Amino Acid Substitution Matrices Find Traces of Ancient Coding Alphabets in Modern Day Proteins
- Protein Structural Phylogenetics
- From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference
- The Lanius excubitor (Aves, Passeriformes) conundrum—Taxonomic dilemma when molecular and non-molecular data tell different stories
- Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation
- Phylogenomic mixture models outperform homogeneous and partitioned models
- Punctuational evolution is pervasive in distal site metastatic colonization
- Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates
- Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms
- Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
- Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology
- The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing
- Pressure-tolerant Evolution in Rhodopsin of Deep-diving Whales
- Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data
- Extracting diamonds: identifiability of 4-node cycles in level-1 phylogenetic networks
- Fast and Accurate Node-Age Estimation Under Fossil Calibration Uncertainty Using the Adjusted Pairwise Likelihood
- A large‐scale phylogeny of the lycophyte genus<i>Selaginella</i>(Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci
- Whole genome shotgun phylogenomics resolve the diving beetle tree of life
- Genome-scale phylogenetic analysis finds extensive gene transfer among\n Fungi
- Molecular clock dating using complex mixture models: applied to ancient symbionts
- Improved Bounds for Context-Dependent Evolutionary Models Using Sequential Monte Carlo
- Terrace Aware Phylogenomic Inference from Supermatrices
- Structural and evolutionary insights into the isoprene monooxygenases
- Modelling compositional and exchange rate changes over time
- Revealing Reassortment in Influenza A Viruses with TreeSort
- Stochastic Mapping of Morphological Characters
- The Identification of Concerted Convergence in Insect Heads Corroborates Palaeoptera
- An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit
- Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data
- Ancestral sequence reconstruction of the Mic60 Mitofilin domain reveals residues supporting respiration in yeast
- When the Past Fades: Detecting Phylogenetic Signal with SatuTe
- A phylogenetic perspective on the evolution of early hominin foot morphology
- CherryML: scalable maximum likelihood estimation of phylogenetic models
- The phylogeny of the Triticeae: Resolution and phylogenetic conflict based on genomewide nuclear loci
- Marked neurotropism and potential adaptation of H5N1 clade 2.3.4.4.b virus in naturally infected domestic cats
- Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways
- The heterogeneous selection landscape of genome evolution in prokaryotes
- Classification of molecular sequence data using Bayesian phylogenetic mixture models
- Evolutionary and immunological implications of contemporary HIV-1 variation
- Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning
- Exploring rates of change and modes of evolution in blastozoan echinoderms
- Million-year-old DNA sheds light on the genomic history of mammoths
- Reconstruction of Ancestral Protein Sequences Using Autoregressive Generative Models
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- PAML 4: Phylogenetic Analysis by Maximum Likelihood
- Likelihood-free inference of phylogenetic tree posterior distributions
- Jurassic avialan reveals stepwise evolution of bony tail in birds
- Biased Estimates of Phylogenetic Branch Lengths Resulting from the Discretised Gamma Model of Site Rate Heterogeneity
- A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
- RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
- Rate Heterogeneity, Ancestral Character State Reconstruction, and the Evolution of Limb Morphology in Lerista (Scincidae, Squamata)
- Bayesian Estimation of Ancestral Character States on Phylogenies
- Probabilistic Graphical Model Representation in Phylogenetics
- RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree
- Phylogenetic Relationships of North American Field Crickets Inferred from Mitochondrial DNA Data
- Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks
- Generalising rate heterogeneity across sites in statistical phylogenetics
- Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation
- The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing
- Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology
- The oldest shark face—anatomy of the Devonian elasmobranch Phoebodus
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation
- A covarion model for phylogenetic estimation using discrete morphological datasets
- piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
- The promise of composite likelihood for species-level phylogenomic inference
- Ultrafast Approximation for Phylogenetic Bootstrap
- Reconstructing Ancient Proteins to Understand the Causes of Structure and Function
- Re-diagnoses of rhinatrematid genera and description of a new species of Guyanese Rhinatrema Duméril & Bibron, 1841 (Amphibia: Gymnophiona: Rhinatrematidae)
- The Winners Take It All? Global Evolutionary Success of H5Nx Reassortants in the 2020–2024 Panzootic
- Quantifying Transcriptome Turnover on Phylogenies by Modeling Gene Expression as a Binary Trait
- Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop
- A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera <i>Aspergillus</i> and <i>Penicillium</i>
- GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics
- Concatenation, Conflict, and Complexity: Genealogical Heterogeneity Mimics Substitutional Heterogeneity for Nucleotide Model Selection
- piqtree: a python package for seamless phylogenetic inference with IQ-TREE
- IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
- A Relaxed Drift Diffusion Model for Phylogenetic Trait Evolution
- Diagnosing Systematic Errors and Incomplete Lineage Sorting in the Deep Phylogeny of Collembola
- Invariant versus classical quartet inference when evolution is\n heterogeneous across sites and lineages
- Importance Sampling Approximation of Sequence Evolution Models with Site-Dependence
- <tt>torchtree</tt> : Flexible Phylogenetic Model Development and Inference Using PyTorch
- Comparing Partition and Mixture Models with Akaike Information Criteria
- W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
- Habitat use affects morphological diversification in dragon lizards