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Measuring Historical and Compositional Signals in Phylogenetic Data

https://doi.org/10.1101/2020.01.03.894097
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What this work says

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

inferredcites →https://doi.org/10.1002/0471650129.dob0534openalex-snapshot
PHYLIP (Phylogeny Inference Package)
inferredcites →https://doi.org/10.1002/9780471650126.dob0534.pub2openalex-snapshot
PHYLIP ( PHYLogeny Inference Package)
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/s10852-005-9017-yopenalex-snapshot
Generation of the Exact Distribution and Simulation of Matched Nucleotide Sequences on a Phylogenetic Tree
inferredcites →https://doi.org/10.1016/j.jtbi.2003.12.010openalex-snapshot
A new criterion and method for amino acid classification
inferredcites →https://doi.org/10.1016/s1055-7903(02)00326-3openalex-snapshot
An index of substitution saturation and its application
inferredcites →https://doi.org/10.1038/srep45302openalex-snapshot
Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil
inferredcites →https://doi.org/10.1073/pnas.0803860105openalex-snapshot
Phylogenetic profiles reveal evolutionary relationships within the “twilight zone” of sequence similarity
inferredcites →https://doi.org/10.1080/01621459.1948.10483284openalex-snapshot
A Test for Symmetry in Contingency Tables
inferredcites →https://doi.org/10.1080/10635150118469openalex-snapshot
Selecting the Best-Fit Model of Nucleotide Substitution
inferredcites →https://doi.org/10.1080/10635150490468648openalex-snapshot
The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
inferredcites →https://doi.org/10.1080/10635150490503035openalex-snapshot
Tracing the Decay of the Historical Signal in Biological Sequence Data
inferredcites →https://doi.org/10.1093/bioinformatics/btl064openalex-snapshot
Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btp368openalex-snapshot
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msm144openalex-snapshot
On Reduced Amino Acid Alphabets for Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
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/nargab/lqaa041openalex-snapshot
A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics
inferredcites →https://doi.org/10.1093/oso/9780198566106.003.0002openalex-snapshot
Likelihood Calculation in Molecular Phylogenetics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025811openalex-snapshot
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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/syu031openalex-snapshot
A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0
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/10.1101/828996openalex-snapshot
Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates
inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot
Phylogenomics resolves the timing and pattern of insect evolution
inferredcites →https://doi.org/10.1177/117693430500100005openalex-snapshot
Estimation of Phylogeny Using a General Markov Model
inferredcites →https://doi.org/10.1371/journal.pcbi.1006650openalex-snapshot
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
inferredcites →https://doi.org/10.2307/3802723openalex-snapshot
Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach

What points at this work

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

inferred← citeshttps://doi.org/10.1002/edn3.70350openalex-snapshot
Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Non‐Bilaterian Animals
inferred← citeshttps://doi.org/10.1093/molbev/msaf090openalex-snapshot
When the Past Fades: Detecting Phylogenetic Signal with SatuTe
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/syac046openalex-snapshot
Assessment of Absolute Substitution Model Fit Accommodating Time-Reversible and Non-Time-Reversible Evolutionary Processes
inferred← citeshttps://doi.org/10.1093/sysbio/syag009openalex-snapshot
The Dayhoff Exchange Score: A New Metric to Quantify Entropic Site Saturation in Amino Acid Data Sets Prior to Phylogenetic Analysis
inferred← citeshttps://doi.org/10.1111/syen.12508openalex-snapshot
Phylogenomic analyses clarify the pattern of evolution of Adephaga (Coleoptera) and highlight phylogenetic artefacts due to model misspecification and excessive data trimming
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
inferred← citeshttps://doi.org/10.59717/j.xinn-life.2026.100235openalex-snapshot
Radiating pattern revealed by a deep learning model traces the evolutionary dynamics of the Archaea domain
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