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Clustering Genes of Common Evolutionary History
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Asymmetrical nature of the T rollius– C hiastocheta interaction: insights into the evolution of nursery pollination systems
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Geometry of the Space of Phylogenetic Trees
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Tree Compatibility and Inferring Evolutionary History
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Speciation in the Globeflower Fly Chiastocheta spp. (Diptera: Anthomyiidae) in Relation to Host Plant Species, Biogeography, and Morphology
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Modeling Gene Family Evolution and Reconciling Phylogenetic Discord
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DLIGHT – Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework
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An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers
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A Metric for Phylogenetic Trees Based on Matching
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
inferredcites →https://doi.org/10.1007/bf00166252openalex-snapshot
Statistical tests of models of DNA substitution
inferredcites →https://doi.org/10.1007/bf02288916openalex-snapshot
Multidimensional Scaling: I. Theory and Method
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Multidimensional Scaling of Similarity
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On the Computational Complexity of the Rooted Subtree Prune and Regraft Distance
inferredcites →https://doi.org/10.1016/0022-5193(74)90100-3openalex-snapshot
Statistical estimation of parameters in a phylogenetic tree using a dynamic model of the substitutional process
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Comparison of phylogenetic trees
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Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
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MOLECULAR STUDIES OF EVOLUTION: A SOURCE OF NOVEL STATISTICAL PROBLEMS**This investigation was supported in part by research grant GM 10525-08 from the National Institutes of Health, Public Health Service.
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Tree disagreement: Measuring and testing incongruence in phylogenies
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Comparing clusterings—an information based distance
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Phylogenomics: the beginning of incongruence?
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The supermatrix approach to systematics
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Coalescent methods for estimating phylogenetic trees
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Ecological and historical drivers of diversification in the fly genus Chiastocheta Pokorny
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Phylogenomics and the reconstruction of the tree of life
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A Model of Horizontal Gene Transfer and the Bacterial Phylogeny Problem
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Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies
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NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees
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Efficiently Computing the Robinson-Foulds Metric
inferredcites →https://doi.org/10.1093/bioinformatics/bth078openalex-snapshot
Open source clustering software
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btq539openalex-snapshot
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
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/bioinformatics/btu121openalex-snapshot
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btu258openalex-snapshot
kdetrees : non-parametric estimation of phylogenetic tree distributions
inferredcites →https://doi.org/10.1093/gbe/evr050openalex-snapshot
Evaluating Phylogenetic Congruence in the Post-Genomic Era
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/genetics/164.4.1645openalex-snapshot
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
inferredcites →https://doi.org/10.1093/molbev/msl051openalex-snapshot
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
inferredcites →https://doi.org/10.1093/molbev/msl170openalex-snapshot
Bayesian Estimation of Concordance among Gene Trees
inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot
Bayesian Inference of Species Trees from Multilocus Data
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Let Them Fall Where They May: Congruence Analysis in Massive Phylogenetically Messy Data Sets
inferredcites →https://doi.org/10.1093/molbev/msr268openalex-snapshot
ALF—A Simulation Framework for Genome Evolution
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Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
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Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution
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An efficient algorithm for large-scale detection of protein families
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A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025813openalex-snapshot
Can three incongruence tests predict when data should be combined?
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.a040126openalex-snapshot
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040517openalex-snapshot
Relationships between gene trees and species trees.
inferredcites →https://doi.org/10.1093/sysbio/42.3.384openalex-snapshot
Partitioning and Combining Data in Phylogenetic Analysis
inferredcites →https://doi.org/10.1093/sysbio/43.2.288openalex-snapshot
Is Character Weighting a Panacea for the Problem of Data Heterogeneity in Phylogenetic Analysis?
inferredcites →https://doi.org/10.1093/sysbio/syr041openalex-snapshot
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes
inferredcites →https://doi.org/10.1093/sysbio/syu084openalex-snapshot
The Phylogenetic Likelihood Library
inferredcites →https://doi.org/10.1098/rstb.1925.0002openalex-snapshot
II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S
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Caloramator viterbensis sp. nov., a novel thermophilic, glycerol-fermenting bacterium isolated from a hot spring in Italy
inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot
Genome-scale coestimation of species and gene trees
inferredcites →https://doi.org/10.1109/tac.1974.1100705openalex-snapshot
A new look at the statistical model identification
inferredcites →https://doi.org/10.1109/tcbb.2010.3openalex-snapshot
A Fast Algorithm for Computing Geodesic Distances in Tree Space
inferredcites →https://doi.org/10.1109/tcbb.2011.157openalex-snapshot
A Metric for Phylogenetic Trees Based on Matching
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Computing the Joint Distribution of Tree Shape and Tree Distance for Gene Tree Inference and Recombination Detection
inferredcites →https://doi.org/10.1109/tpami.2004.1262185openalex-snapshot
Spectral grouping using the nystrom method
inferredcites →https://doi.org/10.1111/1755-0998.12291openalex-snapshot
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
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The phylogeny of a mutualism: evolution and coadaptation between Trollius and its seed-parasitic pollinators
inferredcites →https://doi.org/10.1126/science.1136800openalex-snapshot
Clustering by Passing Messages Between Data Points
inferredcites →https://doi.org/10.1126/science.1250463openalex-snapshot
Statistical binning enables an accurate coalescent-based estimation of the avian tree
inferredcites →https://doi.org/10.1137/110845045openalex-snapshot
Fixed-Parameter Algorithms for Maximum Agreement Forests
inferredcites →https://doi.org/10.1145/369133.369188openalex-snapshot
Efficient algorithms for lateral gene transfer problems
inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150511openalex-snapshot
The (Super)Tree of Life: Procedures, Problems, and Prospects
inferredcites →https://doi.org/10.1186/1471-2105-11-324openalex-snapshot
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
inferredcites →https://doi.org/10.1186/1471-2105-11-s1-s42openalex-snapshot
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
inferredcites →https://doi.org/10.1214/aoms/1177732360openalex-snapshot
The Large-Sample Distribution of the Likelihood Ratio for Testing Composite Hypotheses
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A Bayesian Analysis of Some Nonparametric Problems
inferredcites →https://doi.org/10.1214/aos/1176342871openalex-snapshot
Mixtures of Dirichlet Processes with Applications to Bayesian Nonparametric Problems
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Estimating the Dimension of a Model
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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
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Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
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Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
inferredcites →https://doi.org/10.18637/jss.v053.i09openalex-snapshot
fastcluster : Fast Hierarchical, Agglomerative Clustering Routines for R and Python
inferredcites →https://doi.org/10.2307/sysbio/34.2.193openalex-snapshot
Comparison of Undirected Phylogenetic Trees Based on Subtrees of Four Evolutionary Units
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Scikit-learn: Machine Learning in Python
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Multilocus phylogenetic analysis with gene tree clustering
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Comparative phylotranscriptomics reveals glycolytic adaptation associated with prolonged larval development in the coastal slipper lobster Crenarctus bicuspidatus
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An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets
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Genomic Analysis of Megalocytivirus Genomes Reveals Widespread Recombination
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Peer Review #2 of "DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics (v0.1)"
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Peer Review #3 of "DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics (v0.1)"
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Peer Review #2 of "DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics (v0.2)"
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DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics
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