| scholarly article | Q13442814 |
| P2093 | author name string | M Gouy | |
| N Galtier | |||
| P433 | issue | 7 | |
| P921 | main subject | phylogenetics | Q171184 |
| P304 | page(s) | 871-879 | |
| P577 | publication date | 1998-07-01 | |
| P1433 | published in | Molecular Biology and Evolution | Q1992656 |
| P1476 | title | Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. | |
| P478 | volume | 15 |
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| Q35821681 | A mixed branch length model of heterotachy improves phylogenetic accuracy |
| Q33292268 | A model of evolution with constant selective pressure for regulatory DNA sites. |
| Q34382796 | A new framework for studying the isochore evolution: estimation of the equilibrium GC content based on the temporal mutation rate model |
| Q99965976 | A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries |
| Q52589000 | A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, infered from phylogenetic analysis based on a heterogeneous model of DNA evolution. |
| Q30367472 | A site- and time-heterogeneous model of amino acid replacement. |
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| Q43031065 | Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea |
| Q48039005 | Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). |
| Q34561999 | An empirical examination of the utility of codon-substitution models in phylogeny reconstruction |
| Q37642080 | Analytical Biases Associated with GC-Content in Molecular Evolution |
| Q33303674 | Ancestral inference and the study of codon bias evolution: implications for molecular evolutionary analyses of the Drosophila melanogaster subgroup |
| Q35154658 | Anhydrobiosis and freezing-tolerance: adaptations that facilitate the establishment of Panagrolaimus nematodes in polar habitats |
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| Q35973155 | Arsenophonus and Sodalis Symbionts in Louse Flies: an Analogy to the Wigglesworthia and Sodalis System in Tsetse Flies |
| Q21263052 | Arsenophonus, an emerging clade of intracellular symbionts with a broad host distribution |
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| Q34612854 | Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences |
| Q28742103 | Dynamic evolution of base composition: causes and consequences in avian phylogenomics |
| Q30831807 | EM for phylogenetic topology reconstruction on nonhomogeneous data |
| Q51930405 | Efficient likelihood computations with nonreversible models of evolution. |
| Q44693154 | Endosymbiont phylogenesis in the dryophthoridae weevils: evidence for bacterial replacement |
| Q39758718 | Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss |
| Q58468299 | Estimation of Phylogeny and Invariant Sites under the General Markov Model of Nucleotide Sequence Evolution |
| Q35882363 | Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution |
| Q34908609 | Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition |
| Q46453996 | Evidence for a high ancestral GC content in Drosophila |
| Q40771400 | Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty |
| Q90361739 | Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land? |
| Q35145835 | Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes |
| Q52643008 | Evolutionary history and mode of the amylase multigene family in Drosophila. |
| Q54045634 | Evolving Perceptions on the Antiquity of the Modern Avian Tree |
| Q43029766 | Experimental phylogeny of neutrally evolving DNA sequences generated by a bifurcate series of nested polymerase chain reactions |
| Q28604118 | Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics |
| Q34221682 | Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping |
| Q41865130 | Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model |
| Q33984567 | Functional innovations of three chronological mesohexaploid Brassica rapa genomes |
| Q38601536 | GC-biased gene conversion links the recombination landscape and demography to genomic base composition: GC-biased gene conversion drives genomic base composition across a wide range of species |
| Q34172801 | Gene conversion drives GC content evolution in mammalian histones |
| Q28650847 | Genetic distance for a general non-stationary markov substitution process |
| Q44542979 | Genomic evidence for large, long-lived ancestors to placental mammals |
| Q36238766 | Horizontal gene transfer drives the evolution of Rh50 permeases in prokaryotes |
| Q40500701 | Horizontally acquired genes for purine salvage in Borrelia spp. causing relapsing fever |
| Q34979731 | INDELible: a flexible simulator of biological sequence evolution |
| Q50542006 | Identifying Optimal Models of Evolution. |
| Q89051063 | Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models |
| Q35737610 | Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect |
| Q33654633 | Inference and characterization of horizontally transferred gene families using stochastic mapping |
| Q44343490 | Inference of functional divergence among proteins when the evolutionary process is non-stationary |
| Q33749440 | Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography |
| Q44396836 | Interaction between selection and biased gene conversion in mammalian protein-coding sequence evolution revealed by a phylogenetic covariance analysis |
| Q40332671 | Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages |
| Q24548033 | Isochore evolution in mammals: a human-like ancestral structure |
| Q44312691 | Long-term evolutionary stability of bacterial endosymbiosis in curculionoidea: additional evidence of symbiont replacement in the dryophthoridae family |
| Q52064972 | Maximum-likelihood phylogenetic analysis under a covarion-like model. |
| Q33712502 | Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae). |
| Q36627556 | Model use in phylogenetics: nine key questions. |
| Q33208241 | Modeling compositional heterogeneity |
| Q42056732 | Molecular evolution of the wingless gene and its implications for the phylogenetic placement of the butterfly family Riodinidae (Lepidoptera: papilionoidea). |
| Q44738242 | Molecular phylogeny of the Drosophila melanogaster species subgroup |
| Q33200883 | Monophyly and relationships of wrens (Aves: Troglodytidae): a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data |
| Q34112616 | Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches |
| Q44743305 | Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction |
| Q33371078 | Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs |
| Q52705748 | Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. |
| Q33500837 | PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis |
| Q28657708 | Patterns of positive selection in seven ant genomes |
| Q28740970 | Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood |
| Q36668363 | Phylogenetic analyses of parasites in the new millennium |
| Q45061620 | Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study |
| Q83219625 | Phylogenetic estimation under codon models can be biased by codon usage heterogeneity |
| Q34018081 | Phylogenetic investigation of the genus Raoiella (Prostigmata: Tenuipalpidae): diversity, distribution, and world invasions |
| Q39016750 | Phylogenetic relationships between Sophophora and Lordiphosa, with proposition of a hypothesis on the vicariant divergences of tropical lineages between the Old and New Worlds in the family Drosophilidae |
| Q54660002 | Phylogenetic relationships within the suborder Dermanyssina (Acari: Parasitiformes) and a test of dermanyssoid monophyly |
| Q24652667 | Phylogenomic evidence for multiple losses of flight in ratite birds |
| Q47249240 | Phylogenomics |
| Q40312696 | Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees. |
| Q28247594 | Phylogenomics and the reconstruction of the tree of life |
| Q57077596 | Phylogeny Reconstruction |
| Q46527579 | Phylogeny and molecular evolution of the Drosophila hydei subgroup (Drosophila repleta group) inferred from the Xanthine dehydrogenase gene |
| Q33227261 | Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution |
| Q47840969 | Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution |
| Q24629301 | Phylogeny of gammaproteobacteria |
| Q33199480 | Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences |
| Q34285725 | Probabilistic graphical model representation in phylogenetics |
| Q28607617 | Probabilistic models of eukaryotic evolution: time for integration |
| Q28185340 | RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds |
| Q35081209 | RELAX: detecting relaxed selection in a phylogenetic framework |
| Q34338470 | RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity |
| Q54642051 | Radiation of the ,,Drosophila“ subgenus (Drosophilidae, Diptera) in the Neotropics |
| Q35076941 | Recombination explains isochores in mammalian genomes |
| Q21284108 | Reconstructing the evolutionary history of the radiation of the land snail genus Xerocrassa on Crete based on mitochondrial sequences and AFLP markers |
| Q40778235 | Recreating ancestral proteins |
| Q48608592 | Ribosomal proteins: toward a next generation standard for prokaryotic systematics? |
| Q24799738 | Rooting a phylogenetic tree with nonreversible substitution models |
| Q33322015 | Saturation and base composition bias explain phylogenomic conflict in Plasmodium. |
| Q33236153 | Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree |
| Q43686326 | Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae |
| Q28766408 | Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics |
| Q36273591 | Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data |
| Q50470663 | Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes. |
| Q35038810 | Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome |
| Q29616752 | Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model |
| Q74818920 | Synthetic gene technology: applications to ancestral gene reconstruction and structure-function studies of receptors |
| Q33250586 | Tempo and mode of early gene loss in endosymbiotic bacteria from insects |
| Q55295521 | Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms. |
| Q28659965 | The "naked coral" hypothesis revisited--evidence for and against scleractinian monophyly |
| Q33973441 | The Anolis lizard genome: an amniote genome without isochores |
| Q58468349 | The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated |
| Q57531283 | The Interaction between Base Compositional Heterogeneity and Among-Site Rate Variation in Models of Molecular Evolution |
| Q33983154 | The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network |
| Q35047552 | The bimodal distribution of genic GC content is ancestral to monocot species |
| Q34082007 | The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships |
| Q28285823 | The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny |
| Q47578585 | The effect of non-reversibility on inferring rooted phylogenies |
| Q56876074 | The evolution of base composition and phylogenetic inference |
| Q44592265 | The evolution of genomic base composition in bacteria |
| Q36340826 | The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data. |
| Q33332585 | The impact of recombination on nucleotide substitutions in the human genome |
| Q51995935 | The importance of proper model assumption in bayesian phylogenetics. |
| Q28660511 | The molecular signal for the adaptation to cold temperature during early life on Earth |
| Q28756032 | The perils of plenty: what are we going to do with all these genes? |
| Q36937898 | The quest for natural selection in the age of comparative genomics |
| Q44524056 | The root of the mammalian tree inferred from whole mitochondrial genomes |
| Q22065285 | The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. |
| Q28284337 | Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites |
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| Q46470246 | Transcriptional start site turnover in the evolution of bacterial paralogous genes - the pelE-pelD virulence genes in Dickeya. |
| Q21192750 | Translational machinery of the chaetognath Spadella cephaloptera: a transcriptomic approach to the analysis of cytosolic ribosomal protein genes and their expression |
| Q30381140 | Using non-homogeneous models of nucleotide substitution to identify host shift events: application to the origin of the 1918 'Spanish' influenza pandemic virus. |
| Q58784770 | Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences |
| Q34616500 | Vanishing GC-rich isochores in mammalian genomes. |
| Q57531285 | When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics |
| Q36332268 | Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling |
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