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Using taxon resampling to identify species with contrasting phylogenetic signals: an empirical example in Terrabacteria

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Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups
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Comparison of phylogenetic trees
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The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
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Identification of distinctive molecular traits that are characteristic of the phylum “Deinococcus-Thermus” and distinguish its main constituent groups
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The use of genome-level characters for phylogenetic reconstruction
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Increased sampling of both genes and taxa improves resolution of phylogenetic relationships within Magnoliidae, a large and early-diverging clade of angiosperms
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Genome-scale approaches to resolving incongruence in molecular phylogenies
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Insights into the phylogeny and coding potential of microbial dark matter
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A new view of the tree of life
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Phylogenomics and the reconstruction of the tree of life
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
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Horizontal gene transfer among genomes: The complexity hypothesis
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Increased Taxon Sampling Greatly Reduces Phylogenetic Error
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Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
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How Many Genes Should a Systematist Sample? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence
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Phylogenies and the Comparative Method
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Causes, consequences and solutions of phylogenetic incongruence
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ProtTest 3: fast selection of best-fit models of protein evolution
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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Clustering Genes of Common Evolutionary History
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Database resources of the National Center for Biotechnology Information: update
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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Database Resources of the National Center for Biotechnology Information
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Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista
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Evolutionary relationships of completely sequenced Clostridia species and close relatives
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Proposal for a new classification of a deep branching bacterial phylogenetic lineage: transfer of Coprothermobacter proteolyticus and Coprothermobacter platensis to Coprothermobacteraceae fam. nov., within Coprothermobacterales ord. nov., Coprothermobacteria classis nov. and Coprothermobacterota…
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A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
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Phylogenomic evaluation of members above the species level within the phylum F irmicutes based on conserved proteins
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Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)
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Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context
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Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria
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Proteinortho: Detection of (Co-)orthologs in large-scale analysis
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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
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Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
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The Number of Evolutionary Trees
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Taxon sampling and the accuracy of phylogenetic analyses
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