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Let Them Fall Where They May: Congruence Analysis in Massive Phylogenetically Messy Data Sets

https://doi.org/10.1093/molbev/msr110
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What this work says

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

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Ancient Phylogenetic Relationships
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Computing the nearest neighbor interchange metric for unlabeled binary trees is NP-complete
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Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
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On the Computational Complexity of the Rooted Subtree Prune and Regraft Distance
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Assessing Congruence Among Ultrametric Distance Matrices
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A tutorial on spectral clustering
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Comparison of phylogenetic trees
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Reconstructing reticulate evolutionary histories of plants
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Eubacterial phylogeny based on translational apparatus proteins
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When did the dodo become extinct?
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Horizontal gene transfer among genomes: The complexity hypothesis
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A dendrite method for cluster analysis
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Searching for Convergence in Phylogenetic Markov Chain Monte Carlo
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Testing Congruence in Phylogenomic Analysis
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Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies
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A Rapid Bootstrap Algorithm for the RAxML Web Servers
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Congruence, Consensus, and the Comparative Phylogeography of Codistributed Species in California
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The size of a maximum agreement subtree for random binary trees
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Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
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mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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A congruence index for testing topological similarity between trees
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Empirical profile mixture models for phylogenetic reconstruction
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A practical method for exact computation of subtree prune and regraft distance
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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
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IQPNNI: Moving Fast Through Tree Space and Stopping in Time
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Application of Phylogenetic Networks in Evolutionary Studies
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Phylogenetic Methodology for Detecting Protein Interactions
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Treeness Triangles: Visualizing the Loss of Phylogenetic Signal
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Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny
inferredcites →https://doi.org/10.1093/molbev/msn022openalex-snapshot
Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor
inferredcites →https://doi.org/10.1093/molbev/msq323openalex-snapshot
Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees
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A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
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Archaeal Phylogeny Based on Ribosomal Proteins
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.a026300openalex-snapshot
Rapid Evaluation of the Phylogenetic Congruence of Sequence Data Using Likelihood Ratio Tests
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040189openalex-snapshot
Use of spectral analysis to test hypotheses on the origin of pinnipeds.
inferredcites →https://doi.org/10.1093/sysbio/42.2.126openalex-snapshot
Distributions of Tree Comparison Metrics--Some New Results
inferredcites →https://doi.org/10.1093/sysbio/45.1.92openalex-snapshot
A Likelihood Ratio Test to Detect Conflicting Phylogenetic Signal
inferredcites →https://doi.org/10.1101/gr.114751.110openalex-snapshot
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
inferredcites →https://doi.org/10.1101/sqb.1987.052.01.093openalex-snapshot
Reliability of Evolutionary Trees
inferredcites →https://doi.org/10.1103/physreve.74.036104openalex-snapshot
Finding community structure in networks using the eigenvectors of matrices
inferredcites →https://doi.org/10.1109/t-c.1969.222678openalex-snapshot
A Nonlinear Mapping for Data Structure Analysis
inferredcites →https://doi.org/10.1109/tcbb.2004.44openalex-snapshot
Phylogenetic super-networks from partial trees
inferredcites →https://doi.org/10.1111/1467-9868.00293openalex-snapshot
Estimating the Number of Clusters in a Data Set Via the Gap Statistic
inferredcites →https://doi.org/10.1111/j.1096-0031.1994.tb00181.xopenalex-snapshot
TESTING SIGNIFICANCE OF INCONGRUENCE
inferredcites →https://doi.org/10.1111/j.1558-5646.1983.tb05528.xopenalex-snapshot
TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
inferredcites →https://doi.org/10.1126/science.278.5338.631openalex-snapshot
A Genomic Perspective on Protein Families
inferredcites →https://doi.org/10.1146/annurev.ps.46.020195.003021openalex-snapshot
Multiple Hypothesis Testing
inferredcites →https://doi.org/10.1186/1471-2148-11-64openalex-snapshot
The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis
inferredcites →https://doi.org/10.1186/1471-2148-7-7openalex-snapshot
Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika – the result of repeated introgressive hybridization
inferredcites →https://doi.org/10.1186/1745-6150-4-34openalex-snapshot
Prokaryotic evolution and the tree of life are two different things
inferredcites →https://doi.org/10.1186/gb-2007-8-8-r156openalex-snapshot
Complexity, connectivity, and duplicability as barriers to lateral gene transfer
inferredcites →https://doi.org/10.1186/jbiol159openalex-snapshot
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
inferredcites →https://doi.org/10.2307/1402306openalex-snapshot
Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability; Vol. IV
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Comparison of Undirected Phylogenetic Trees Based on Subtrees of Four Evolutionary Units

What points at this work

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

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