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The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ajb2.1152openalex-snapshot
Order‐level fern plastome phylogenomics: new insights from Hymenophyllales
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/bf00486096openalex-snapshot
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
inferredcites →https://doi.org/10.1007/s00239-007-9062-4openalex-snapshot
Topological Estimation Biases with Covarion Evolution
inferredcites →https://doi.org/10.1016/j.gene.2006.02.023openalex-snapshot
Assessing the microsporidia-fungi relationship: Combined phylogenetic analysis of eight genes
inferredcites →https://doi.org/10.1038/nature02917openalex-snapshot
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
inferredcites →https://doi.org/10.1038/nature09864openalex-snapshot
Phylogenomic analyses unravel annelid evolution
inferredcites →https://doi.org/10.1038/nature10382openalex-snapshot
Phylogenomics reveals deep molluscan relationships
inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot
Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1073/pnas.0603797103openalex-snapshot
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1073/pnas.1503453112openalex-snapshot
Error, signal, and the placement of Ctenophora sister to all other animals
inferredcites →https://doi.org/10.1073/pnas.1518127112openalex-snapshot
Genomic data do not support comb jellies as the sister group to all other animals
inferredcites →https://doi.org/10.1073/pnas.1525332113openalex-snapshot
Miscues misplace sponges
inferredcites →https://doi.org/10.1080/10635150390235395openalex-snapshot
Estimation of Rates-Across-Sites Distributions in Phylogenetic Substitution Models
inferredcites →https://doi.org/10.1080/10635150500234609openalex-snapshot
An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics
inferredcites →https://doi.org/10.1080/10635150590946808openalex-snapshot
Partitioned Bayesian Analyses, Partition Choice, and the Phylogenetic Relationships of Scincid Lizards
inferredcites →https://doi.org/10.1080/10635150701546249openalex-snapshot
The Importance of Data Partitioning and the Utility of Bayes Factors in Bayesian Phylogenetics
inferredcites →https://doi.org/10.1093/bioinformatics/btn445openalex-snapshot
Empirical profile mixture models for phylogenetic reconstruction
inferredcites →https://doi.org/10.1093/gbe/evy205openalex-snapshot
Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium
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/molbev/msh112openalex-snapshot
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
inferredcites →https://doi.org/10.1093/molbev/msi123openalex-snapshot
Likelihood, Parsimony, and Heterogeneous Evolution
inferredcites →https://doi.org/10.1093/molbev/msn067openalex-snapshot
An Improved General Amino Acid Replacement Matrix
inferredcites →https://doi.org/10.1093/molbev/mss020openalex-snapshot
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/mss112openalex-snapshot
Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates
inferredcites →https://doi.org/10.1093/molbev/msu044openalex-snapshot
An Amino Acid Substitution-Selection Model Adjusts Residue Fitness to Improve Phylogenetic Estimation
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msv026openalex-snapshot
The Effects of Partitioning on Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msw171openalex-snapshot
Extensively Parameterized Mutation–Selection Models Reliably Capture Site-Specific Selective Constraint
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003973openalex-snapshot
Heterotachy, an Important Process of Protein Evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004053openalex-snapshot
Combining Multiple Data Sets in a Likelihood Analysis: Which Models are the Best?
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025995openalex-snapshot
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies
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/sysbio/44.1.17openalex-snapshot
Performance of Phylogenetic Methods in Simulation
inferredcites →https://doi.org/10.1093/sysbio/syq002openalex-snapshot
Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial
inferredcites →https://doi.org/10.1093/sysbio/syt022openalex-snapshot
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
inferredcites →https://doi.org/10.1093/sysbio/syv059openalex-snapshot
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny
inferredcites →https://doi.org/10.1093/sysbio/syw037openalex-snapshot
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
inferredcites →https://doi.org/10.1093/sysbio/syx068openalex-snapshot
Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
inferredcites →https://doi.org/10.1093/sysbio/syx092openalex-snapshot
Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model
inferredcites →https://doi.org/10.1093/sysbio/syx097openalex-snapshot
Information Criteria for Comparing Partition Schemes
inferredcites →https://doi.org/10.1093/sysbio/syy061openalex-snapshot
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods
inferredcites →https://doi.org/10.1098/rspb.2013.1755openalex-snapshot
Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads
inferredcites →https://doi.org/10.1098/rstb.2008.0180openalex-snapshot
Phylogenetic mixture models for proteins
inferredcites →https://doi.org/10.1109/tac.1974.1100705openalex-snapshot
A new look at the statistical model identification
inferredcites →https://doi.org/10.1111/j.1463-6409.2012.00551.xopenalex-snapshot
Exploration of data partitioning in an eight‐gene data set: phylogeny of metalmark moths (Lepidoptera, Choreutidae)
inferredcites →https://doi.org/10.1186/1471-2148-14-82openalex-snapshot
Selecting optimal partitioning schemes for phylogenomic datasets
inferredcites →https://doi.org/10.1186/1471-2148-7-s1-s4openalex-snapshot
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
inferredcites →https://doi.org/10.1186/1471-2148-8-331openalex-snapshot
A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny
inferredcites →https://doi.org/10.1371/journal.pone.0022783openalex-snapshot
Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
inferredcites →https://doi.org/10.2202/1544-6115.1626openalex-snapshot
Large Sample Approximations of Probabilities of Correct Evolutionary Tree Estimation and Biases of Maximum Likelihood Estimation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1016/j.ympev.2025.108348openalex-snapshot
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Phylogenomic analysis resolves the evolutionary pattern of diversification of cyanobacteria and reveals the evolutionary affinity of novel Antarctic lineages
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Assessing the validity of the two-subfamily system in the Nemouridae: An integrated taxonomic approach
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Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding
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Available data do not rule out Ctenophora as the sister group to all other Metazoa
inferred← citeshttps://doi.org/10.1073/pnas.2408775121openalex-snapshot
Revisiting the four Hexapoda classes: Protura as the sister group to all other hexapods
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Mitogenomic phylogeny and timetree of Trematoda: overcoming topological instability
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A Practical Guide to Design and Assess a Phylogenomic Study
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CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora
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Six Newly Sequenced Chloroplast Genomes From Quadriflagellate Chlamydomonadales (Chlorophyceae): Phylogeny and Comparative Genome Analyses
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Phylogenomic insights into the higher level relationships within Culicomorpha (Diptera) revealed by whole-genome sequencing
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inferred← citeshttps://doi.org/10.1101/810309openalex-snapshot
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Evolutionary Trajectory of the Replication Mode of Bacterial Replicons
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inferred← citeshttps://doi.org/10.1186/s12915-022-01297-0openalex-snapshot
Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family
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A PHYLOGENOMIC APPROACH TO EXPLORE PHOTOSYNTHETHIC STRAMENOPILE EVOLUTION
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Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae
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Polyphyly of Boehmeria (Urticaceae) congruent with plastome structural variation
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inferred← citeshttps://doi.org/10.3390/jof12090654openalex-snapshot
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Additional file 12 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443009openalex-snapshot
Additional file 14 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443018openalex-snapshot
Additional file 16 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443021openalex-snapshot
Additional file 17 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443024openalex-snapshot
Additional file 18 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443030openalex-snapshot
Additional file 2 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443033openalex-snapshot
Additional file 3 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443036openalex-snapshot
Additional file 4 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443039openalex-snapshot
Additional file 5 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443042openalex-snapshot
Additional file 6 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443045openalex-snapshot
Additional file 7 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443048openalex-snapshot
Additional file 8 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.14443051openalex-snapshot
Additional file 9 of Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans
inferred← citeshttps://doi.org/10.6084/m9.figshare.19654525openalex-snapshot
Additional file 1 of Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family
inferred← citeshttps://doi.org/10.6084/m9.figshare.19654534openalex-snapshot
Additional file 2 of Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family
inferred← citeshttps://doi.org/10.6084/m9.figshare.19654537openalex-snapshot
Additional file 3 of Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family
inferred← citeshttps://doi.org/10.64898/2026.03.16.712229openalex-snapshot
A New Information Theoretic Approach Shows that Mixture Models Outperform Partitioned Models for Phylogenetic Analyses of Amino Acid Data
inferred← citeshttps://doi.org/10.70675/2ec65bcazc401z4c3bz943fzbffd552991d2openalex-snapshot
Datations dans les arbres de gènes : spéciations, duplications, pertes
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