| scholarly article | Q13442814 |
| P2093 | author name string | Peter G Foster | |
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| P433 | issue | 3 | |
| P921 | main subject | heterogeneity | Q928498 |
| P304 | page(s) | 485-495 | |
| P577 | publication date | 2004-06-01 | |
| P1433 | published in | Systematic Biology | Q7663761 |
| P1476 | title | Modeling compositional heterogeneity | |
| P478 | volume | 53 |
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| Q28606353 | A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology |
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| Q55129585 | A congruent phylogenomic signal places eukaryotes within the Archaea. |
| Q64025759 | A congruent topology for deep gastropod relationships |
| Q90136167 | A first phylogenetic study on stoloniferous octocorals off the coast of Kota Kinabalu, Sabah, Malaysia, with the description of two new genera and five new species |
| Q64272778 | A haplotype-resolved draft genome of the European sardine (Sardina pilchardus) |
| Q34631297 | A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases |
| Q35821681 | A mixed branch length model of heterotachy improves phylogenetic accuracy |
| Q27496564 | A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies |
| Q57011290 | A phylogeny of Vesiculariidae (Bryozoa, Ctenostomata) supports synonymization of three genera and reveals possible cryptic diversity |
| Q34026101 | A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade |
| Q35290567 | A rooted net of life. |
| Q30367472 | A site- and time-heterogeneous model of amino acid replacement. |
| Q42618478 | Accounting for gene rate heterogeneity in phylogenetic inference |
| Q43031065 | Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea |
| Q34190649 | Adding resolution to ordinal level relationships of tapeworms (Platyhelminthes: Cestoda) with large fragments of mtDNA. |
| Q48039005 | Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). |
| Q35731764 | An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees |
| Q34391778 | An archaeal origin of eukaryotes supports only two primary domains of life |
| Q40489041 | An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree. |
| Q64104433 | An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins |
| Q33556630 | Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants |
| Q46286607 | Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families. |
| Q37642080 | Analytical Biases Associated with GC-Content in Molecular Evolution |
| Q50082506 | Archaea and the origin of eukaryotes. |
| Q28645661 | Are flatfishes (Pleuronectiformes) monophyletic? |
| Q53019438 | Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly. |
| Q46984377 | Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton |
| Q35935845 | Assessing the performance of DNA barcoding using posterior predictive simulations. |
| Q29617331 | Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified |
| Q34310772 | Assessment of substitution model adequacy using frequentist and Bayesian methods |
| Q46240577 | Bayesian molecular dating: opening up the black box. |
| Q28749030 | Bayesian random local clocks, or one rate to rule them all |
| Q51968312 | Biases in phylogenetic estimation can be caused by random sequence segments. |
| Q38047777 | Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences. |
| Q56975259 | Building trees of algae: some advances in phylogenetic and evolutionary analysis |
| Q35164225 | Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea) |
| Q21283857 | Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships |
| Q38367980 | Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data? |
| Q33283632 | Chloroplast His-to-Asp signal transduction: a potential mechanism for plastid gene regulation in Heterosigma akashiwo (Raphidophyceae) |
| Q52979684 | Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. |
| Q34431575 | Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies |
| Q43455802 | Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations |
| Q30378791 | Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives. |
| Q33388542 | Comparison of methods for estimating the nucleotide substitution matrix |
| Q33830158 | Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura |
| Q52880907 | Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). |
| Q33801888 | Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins |
| Q91436913 | Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants |
| Q33552016 | Compositional heterogeneity and phylogenomic inference of metazoan relationships |
| Q28659001 | Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions |
| Q39231113 | Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling |
| Q36031512 | Cross-validation to select Bayesian hierarchical models in phylogenetics |
| Q28314979 | Cryptic carbon and sulfur cycling between surface ocean plankton |
| Q36301357 | Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes. |
| Q21092303 | DNA-sequence variation among Schistosoma mekongi populations and related taxa; phylogeography and the current distribution of Asian schistosomiasis |
| Q52562743 | Deep mitochondrial origin outside the sampled alphaproteobacteria. |
| Q58634200 | Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies |
| Q45158968 | Detection of implausible phylogenetic inferences using posterior predictive assessment of model fit. |
| Q55251055 | Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy. |
| Q92239421 | Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons |
| Q35026156 | Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva |
| Q51892918 | Does choice in model selection affect maximum likelihood analysis? |
| Q39492472 | Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. |
| Q51930405 | Efficient likelihood computations with nonreversible models of evolution. |
| Q64059045 | Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes |
| Q58468299 | Estimation of Phylogeny and Invariant Sites under the General Markov Model of Nucleotide Sequence Evolution |
| Q34229048 | Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. |
| Q28760077 | Estimation of phylogeny using a general Markov model |
| Q26795691 | Eukaryotic origins |
| Q40748980 | Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations |
| Q30786867 | Evaluating topological conflict in centipede phylogeny using transcriptomic data sets |
| Q35882363 | Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution |
| Q28686918 | Evolution of divergent life history strategies in marine alphaproteobacteria |
| Q33237185 | Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes |
| Q56698938 | Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses |
| Q33801686 | Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters |
| Q34592403 | Evolutionary ecology of the marine Roseobacter clade |
| Q40870401 | Evolutionary origin of a streamlined marine bacterioplankton lineage |
| Q31027366 | Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa |
| Q28604118 | Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics |
| Q33411609 | First molecular estimate of cyclostome bryozoan phylogeny confirms extensive homoplasy among skeletal characters used in traditional taxonomy |
| Q41865130 | Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model |
| Q21089841 | Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling |
| Q28658690 | From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes |
| Q92538627 | Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human |
| Q29010741 | Genomic Support for a Moa-Tinamou Clade and Adaptive Morphological Convergence in Flightless Ratites |
| Q28681724 | Heterogeneous models place the root of the placental mammal phylogeny |
| Q33675296 | Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny |
| Q28607620 | Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis |
| Q50542006 | Identifying Optimal Models of Evolution. |
| Q33212839 | Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda |
| Q28608229 | Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics |
| Q28755823 | Improvement of molecular phylogenetic inference and the phylogeny of Bilateria |
| Q41670546 | Improvement of phylogenetic method to analyze compositional heterogeneity |
| Q89051063 | Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models |
| Q28247426 | Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade |
| Q33749440 | Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography |
| Q90646636 | Inferring tunicate relationships and the evolution of the tunicate Hox cluster with the genome of Corella inflata |
| Q33940838 | Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses |
| Q40332671 | Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages |
| Q48063926 | MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment |
| Q33474810 | Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences |
| Q33512008 | Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests |
| Q30528537 | Metazoan opsin evolution reveals a simple route to animal vision |
| Q92705227 | Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda |
| Q28741416 | Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes |
| Q91386612 | Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species |
| Q44211861 | Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships |
| Q30833797 | Mitogenomic data resolve basal relationships among passeriform and passeridan birds |
| Q37089708 | Models of coding sequence evolution |
| Q36259364 | Molecular Phylogeny of Neotropical Anopheles (Nyssorhynchus) Albitarsis Species Complex (Diptera: Culicidae). |
| Q43648326 | Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology |
| Q110697158 | Molecular phylogeny of the orb-weaving spider genus Leucauge and the intergeneric relationships of Leucauginae (Araneae, Tetragnathidae) |
| Q47409100 | Monte Carlo Strategies for Selecting Parameter Values in Simulation Experiments |
| Q98831088 | Most Cephalaspidea have a shell, but transcriptomes can provide them with a backbone (Gastropoda: Heterobranchia) |
| Q36316116 | Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini). |
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| Q34112616 | Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches |
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| Q38883886 | New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity |
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| Q41834056 | New substitution models for rooting phylogenetic trees |
| Q36046489 | Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny |
| 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. |
| Q28649621 | Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation |
| Q88054160 | On how many fundamental kinds of cells are present on Earth: looking for phylogenetic traits that would allow the identification of the primary lines of descent |
| Q36042851 | Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). |
| Q30855762 | Pathological rate matrices: from primates to pathogens |
| Q33742087 | Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes |
| Q33652954 | Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets |
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| Q30587303 | Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus). |
| 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 |
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| Q28647434 | Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants |
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| Q21093408 | Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support |
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| Q34443578 | Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids. |
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| Q28247594 | Phylogenomics and the reconstruction of the tree of life |
| Q91826581 | Phylogenomics provides robust support for a two-domains tree of life |
| Q47137478 | Phylogeny of Anophelinae using mitochondrial protein coding genes |
| Q110951047 | Phylogeny of Globba section Nudae and taxonomic revision of the new Globba subsection Pelecantherae |
| Q37841537 | Plastid establishment did not require a chlamydial partner |
| Q37701019 | Posterior predictive Bayesian phylogenetic model selection |
| Q28607617 | Probabilistic models of eukaryotic evolution: time for integration |
| Q110949515 | Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics |
| Q36525066 | Quantifying homologous replacement of loci between haloarchaeal species. |
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| Q111630359 | Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons |
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| Q67234679 | Revisiting metazoan phylogeny with genomic sampling of all phyla |
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| Q34298522 | Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study |
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| Q28741772 | Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods |
| Q36115242 | Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection |
| Q58566883 | Stolonifera from shallow waters in the north-western Pacific: a description of a new genus and two new species within the Arulidae (Anthozoa, Octocorallia) |
| Q50470663 | Streptophyte algae and the origin of land plants revisited using heterogeneous models with three new algal chloroplast genomes. |
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| Q62050368 | The complete mitogenome of Helix pomatia and the basal phylogeny of Helicinae (Gastropoda, Stylommatophora, Helicidae) |
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| Q33394139 | The eocyte hypothesis and the origin of eukaryotic cells |
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| Q87845427 | The hybrid nature of the Eukaryota and a consilient view of life on Earth |
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| Q28752077 | The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods |
| Q28082357 | The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data |
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| Q51898474 | Topological estimation biases with covarion evolution. |
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| 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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