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Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates

https://doi.org/10.1101/828996
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What this work says

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

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Phylogenetic inference from conserved sites alignments
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PHYLIP (Phylogeny Inference Package)
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Proportions, Percentages, PPM: Do the Molecular Biosciences Treat Compositional Data Right?
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Basic Concepts and Procedures
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General Time-Reversible Distances with Unequal Rates across Sites: Mixing Γ and Inverse Gaussian Distributions with Invariant Sites
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SeqVis: A Tool for Detecting Compositional Heterogeneity Among Aligned Nucleotide Sequences
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The Statistical Analysis of Compositional Data
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Statistical tests of models of DNA substitution
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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Generation of the Exact Distribution and Simulation of Matched Nucleotide Sequences on a Phylogenetic Tree
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Comparison of phylogenetic trees
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Progress with methods for constructing evolutionary trees
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Recovering a tree from the leaf colourations it generates under a Markov model
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A new criterion and method for amino acid classification
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Fixed, free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian–Triassic origin
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The evolution of base composition and phylogenetic inference
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Reduced Thermophilic Bias in the 16S rDNA Sequence from Thermus ruber Provides Further Support for a Relationship Between Thermus and Deinococcus
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Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
inferredcites →https://doi.org/10.1038/nature08064openalex-snapshot
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
inferredcites →https://doi.org/10.1073/pnas.91.4.1455openalex-snapshot
Reconstructing evolutionary trees from DNA and proteinsequences: paralinear distances.
inferredcites →https://doi.org/10.1073/pnas.92.24.11317openalex-snapshot
Inferring phylogenies from DNA sequences of unequal base compositions.
inferredcites →https://doi.org/10.1080/01621459.1948.10483284openalex-snapshot
A Test for Symmetry in Contingency Tables
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Modeling Compositional Heterogeneity
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The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
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Tracing the Decay of the Historical Signal in Biological Sequence Data
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Estimation of Phylogeny and Invariant Sites under the General Markov Model of Nucleotide Sequence Evolution
inferredcites →https://doi.org/10.1080/106351599260427openalex-snapshot
Using Novel Phylogenetic Methods to Evaluate Mammalian mtDNA, Including Amino Acid-Invariant Sites-LogDet plus Site Stripping, to Detect Internal Conflicts in the Data, with Special Reference to the Positions of Hedgehog, Armadillo, and Elephant
inferredcites →https://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
inferredcites →https://doi.org/10.1093/bib/bbz016openalex-snapshot
Sensitivity and specificity of information criteria
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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
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A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
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Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
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tqDist: a library for computing the quartet and triplet distances between binary or general trees
inferredcites →https://doi.org/10.1093/biomet/42.3-4.412openalex-snapshot
A TEST FOR HOMOGENEITY OF THE MARGINAL DISTRIBUTIONS IN A TWO-WAY CLASSIFICATION
inferredcites →https://doi.org/10.1093/biomet/69.3.493openalex-snapshot
Plots of P-values to evaluate many tests simultaneously
inferredcites →https://doi.org/10.1093/gbe/evy094openalex-snapshot
Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy
inferredcites →https://doi.org/10.1093/gbe/evz193openalex-snapshot
The Prevalence and Impact of Model Violations in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/molbev/msh018openalex-snapshot
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot
Application of Phylogenetic Networks in Evolutionary Studies
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On Reduced Amino Acid Alphabets for Phylogenetic Inference
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Using Data-Display Networks for Exploratory Data Analysis in Phylogenetic Studies
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/msv150openalex-snapshot
FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.
inferredcites →https://doi.org/10.1093/molbev/msx092openalex-snapshot
New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025808openalex-snapshot
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040136openalex-snapshot
Recovering evolutionary trees under a more realistic model of sequence evolution.
inferredcites →https://doi.org/10.1093/sysbio/42.3.247openalex-snapshot
Success of Phylogenetic Methods in the Four-Taxon Case
inferredcites →https://doi.org/10.1093/sysbio/syu036openalex-snapshot
Mixture Models of Nucleotide Sequence Evolution that Account for Heterogeneity in the Substitution Process Across Sites and Across Lineages
inferredcites →https://doi.org/10.1093/sysbio/syu085openalex-snapshot
Practical Performance of Tree Comparison Metrics
inferredcites →https://doi.org/10.1126/science.269.5222.363openalex-snapshot
John Merlie (1945-1995)
inferredcites →https://doi.org/10.1126/science.8171318openalex-snapshot
Application and Accuracy of Molecular Phylogenies
inferredcites →https://doi.org/10.1177/117693430500100005openalex-snapshot
Estimation of Phylogeny Using a General Markov Model
inferredcites →https://doi.org/10.1186/1471-2105-15-s2-s8openalex-snapshot
Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics
inferredcites →https://doi.org/10.2307/1218253openalex-snapshot
ON THE COMPARISON OF TWO CLASSIFICATIONS OF THE SAME SET OF ELEMENTS
inferredcites →https://doi.org/10.2307/1270335openalex-snapshot
The Statistical Analysis of Compositional Data

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s10750-023-05451-9openalex-snapshot
Whole-genome analyses converge to support the Hemirotifera hypothesis within Syndermata (Gnathifera)
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/sysbio/syab013openalex-snapshot
Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae)
inferred← citeshttps://doi.org/10.1101/2020.01.03.894097openalex-snapshot
Measuring Historical and Compositional Signals in Phylogenetic Data
inferred← citeshttps://doi.org/10.3389/fpls.2020.01062openalex-snapshot
The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models
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