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Experimental Design in Phylogenetics: Testing Predictions from Expected Information

https://doi.org/10.1093/sysbio/sys028
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Information Theory and an Extension of the Maximum Likelihood Principle
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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The comparative morphology and evolution of the eyes of caecilians (Amphibia, Gymnophiona)
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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CHARACTERS, CONGRUENCE AND QUALITY: A STUDY OF NEUROANATOMICAL AND TRADITIONAL DATA IN CAECILIAN PHYLOGENY
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Taxon sampling revisited
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Global patterns of diversification in the history of modern amphibians
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Incomplete taxon sampling is not a problem for phylogenetic inference
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Systematics and ecology of the caecilianCrotaphatrema lamottei(Nussbaum) (Amphibia: Gymnophiona: Scolecomorphidae)
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An Approximately Unbiased Test of Phylogenetic Tree Selection
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Increased Taxon Sampling Greatly Reduces Phylogenetic Error
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Increased Taxon Sampling Is Advantageous for Phylogenetic Inference
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Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?
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Mitogenomic Perspectives on the Origin and Phylogeny of Living Amphibians
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Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
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Experimental Design Criteria in Phylogenetics: Where to Add Taxa
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Taxon Sampling and the Accuracy of Large Phylogenies
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Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias
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Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?
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Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators
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Phylogenetic relationships of African caecilians (Amphibia: Gymnophiona): Insights from mitochondrial rRNA gene sequences
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Initial Diversification of Living Amphibians Predated the Breakup of Pangaea
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The performance of the neighbor-joining method of phylogeny reconstruction
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Recent developments in the MAFFT multiple sequence alignment program
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EDIBLE: experimental design and information calculations in phylogenetics
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CONSEL: for assessing the confidence of phylogenetic tree selection
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MRBAYES: Bayesian inference of phylogenetic trees
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The rapid generation of mutation data matrices from protein sequences
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MrBayes 3: Bayesian phylogenetic inference under mixed models
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ProtTest: selection of best-fit models of protein evolution
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
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More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy
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MtArt: A New Model of Amino Acid Replacement for Arthropoda
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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jModelTest: Phylogenetic Model Averaging
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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
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TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
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Models of amino acid substitution and applications to mitochondrial protein evolution
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Mitochondrial Genes and Mammalian Phylogenies: Increasing the Reliability of Branch Length Estimation
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Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
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An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
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Maximum Likelihood Trees from DNA Sequences: A Peculiar Statistical Estimation Problem
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Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1
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Phylogenetic information and experimental design in molecular systematics
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The heart and aortic arches of rhinatrematid caecilians (Amphibia: Gymnophiona)
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CHARACTERS, CONGRUENCE AND QUALITY: A STUDY OF NEUROANATOMICAL AND TRADITIONAL DATA IN CAECILIAN PHYLOGENY
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Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
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The phylogenetic position of the Rhinatrematidae (Amphibia: Gymnophiona): evidence from the larval lateral line system
inferredcites →https://doi.org/10.11646/zootaxa.2767.1.2openalex-snapshot
The systematics of Boulengerula fischeri (Amphibia: Gymnophiona: Caeciliidae) based on morphological and molecular data
inferredcites →https://doi.org/10.11646/zootaxa.2874.1.3openalex-snapshot
A nine-family classification of caecilians (Amphibia: Gymnophiona)
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PhyDesign: an online application for profiling phylogenetic informativeness
inferredcites →https://doi.org/10.1201/9781482280142openalex-snapshot
Reproductive Biology and Phylogeny of Gymnophiona: Caecilians
inferredcites →https://doi.org/10.1201/9781482280142-8openalex-snapshot
Caecilian Phylogeny and Classification
inferredcites →https://doi.org/10.1206/0003-0090(2006)297[0001:tatol]2.0.co;2openalex-snapshot
THE AMPHIBIAN TREE OF LIFE
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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.2307/1447519openalex-snapshot
On the Phylogenetic Position of the Uraeotyphlidae (Amphibia: Gymnophiona)
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Caecilian Phylogeny and Biogeography Inferred from Mitochondrial DNA Sequences of the 12S rRNA and 16S rRNA Genes (Amphibia: Gymnophiona)
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On the Classification and Phylogeny of Caecilians (Amphibia: Gymnophiona), a Critical Review
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An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
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Molecular systematics: A synthesis of the common methods and the state of knowledge

What points at this work

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

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Additional file 1 of Quantification and evolution of mitochondrial genome rearrangement in Amphibians
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