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Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases

https://doi.org/10.1093/molbev/msg115
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What this work says

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

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A few logs suffice to build (almost) all trees (I)
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A few logs suffice to build (almost) all trees (I)
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Phylogenetic Inference
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Genome trees and the tree of life
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Phylogenetic supertrees: Assembling the trees of life
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Parallel adaptive radiations in two major clades of placental mammals
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Molecular phylogenetics and the origins of placental mammals
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Inferring complex phytogenies
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Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
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Universal trees based on large combined protein sequence data sets
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The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium , Entamoeba , and Mastigamoeba
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Toward Understanding Anophelinae (Diptera, Culicidae) Phylogeny: Insights from Nuclear Single-Copy Genes and the Weight of Evidence
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Fragmentary Taxa, Missing Data, and Ambiguity: Mistaken Assumptions and Conclusions
inferredcites →https://doi.org/10.1080/106351598260635openalex-snapshot
Does Adding Characters with Missing Data Increase or Decrease Phylogenetic Accuracy?
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Inferring Complex Phylogenies Using Parsimony: An Empirical Approach Using Three Large DNA Data Sets for Angiosperms
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Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences
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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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The SYSTERS protein sequence cluster set
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The COG database: new developments in phylogenetic classification of proteins from complete genomes
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CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
inferredcites →https://doi.org/10.1093/sysbio/27.4.401openalex-snapshot
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
inferredcites →https://doi.org/10.1093/sysbio/42.3.384openalex-snapshot
Partitioning and Combining Data in Phylogenetic Analysis
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Multiple Sources of Character Information and the Phylogeny of Hawaiian Drosophilids
inferredcites →https://doi.org/10.1093/sysbio/49.2.306openalex-snapshot
Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences
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Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)
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Molecular and Morphological Supertrees for Eutherian (Placental) Mammals
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SCALING OF ACCURACY IN EXTREMELY LARGE PHYLOGENETIC TREES
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Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL
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Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
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Multiple Sources of Character Information and the Phylogeny of Hawaiian Drosophilids
inferredcites →https://doi.org/10.2307/2656749openalex-snapshot
Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms

What points at this work

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

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STBase: One Million Species Trees for Comparative Biology
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Efficient Mining of Maximal Bicliques in Graph by Pruning Search Space
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Faculty Opinions recommendation of The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.
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Missing data and the accuracy of Bayesian phylogenetics
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Molecular data from 27 proteins do not support a Precambrian origin of land plants
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Palaeoheterodont Phylogeny, Character Evolution, Diversity and Phylogenetic Classification: A Reflection on Methods of Analysis
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Enumerating Maximal Bicliques from a Large Graph using MapReduce
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On the Phase Transition of Finding a Biclique in a larger Bipartite Graph
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A Change-Sensitive Algorithm for Maintaining Maximal Bicliques in a Dynamic Bipartite Graph
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The quest for orthologs, the tree of basal animals, and taxonomic profiles of metagenomes
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Méthodes combinatoires de reconstruction de réseaux phylogénétiques
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