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Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Finding Optimal Ingroup Topologies and Convexities When the Choice of Outgroups Is Not Obvious
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats
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Genome-scale DNA sequence data and the evolutionary history of placental mammals
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Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera
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Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
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Phylogenetic rooting using minimal ancestor deviation
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Evaluating alternative hypotheses for the early evolution and diversification of ants
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Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
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Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
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Error, signal, and the placement of Ctenophora sister to all other animals
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Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
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Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals
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Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
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Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.
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Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins.
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Inferring the Root of a Phylogenetic Tree
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An Approximately Unbiased Test of Phylogenetic Tree Selection
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Examining Basal Avian Divergences with Mitochondrial Sequences: Model Complexity, Taxon Sampling, and Sequence Length
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Estimating Phylogenetic Trees from Distance Matrices
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Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles
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The rapid generation of mutation data matrices from protein sequences
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
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New Methods to Calculate Concordance Factors for Phylogenomic Datasets
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The Protistan Origins of Animals and Fungi
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Rooting the Tree of Life Using Nonubiquitous Genes
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An Improved General Amino Acid Replacement Matrix
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Quantifying the Stationarity and Time Reversibility of the Nucleotide Substitution Process
inferredcites →https://doi.org/10.1093/molbev/msr128openalex-snapshot
Reducing Model Complexity of the General Markov Model of Evolution
inferredcites →https://doi.org/10.1093/molbev/msx294openalex-snapshot
The Effect of Nonreversibility on Inferring Rooted Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msz291openalex-snapshot
Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference
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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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Rooting Phylogenetic Trees with Distant Outgroups: A Case Study from the Commelinoid Monocots
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
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Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040220openalex-snapshot
On the use of nucleic acid sequences to infer early branchings in the tree of life.
inferredcites →https://doi.org/10.1093/sysbio/30.1.1openalex-snapshot
The Out-Group Comparison Method of Character Analysis
inferredcites →https://doi.org/10.1093/sysbio/33.1.83openalex-snapshot
Outgroup Analysis and Parsimony
inferredcites →https://doi.org/10.1093/sysbio/syw037openalex-snapshot
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
inferredcites →https://doi.org/10.1098/rstb.2014.0336openalex-snapshot
New substitution models for rooting phylogenetic trees
inferredcites →https://doi.org/10.1099/00207713-51-2-385openalex-snapshot
A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data.
inferredcites →https://doi.org/10.1101/460121openalex-snapshot
The Prevalence and Impact of Model Violations in Phylogenetics Analysis
inferredcites →https://doi.org/10.1101/gr.141978.112openalex-snapshot
Genome-scale coestimation of species and gene trees
inferredcites →https://doi.org/10.1111/j.1095-8312.1994.tb00962.xopenalex-snapshot
Rooting molecular trees: problems and strategies
inferredcites →https://doi.org/10.1126/science.1078607openalex-snapshot
Hexapod Origins: Monophyletic or Paraphyletic?
inferredcites →https://doi.org/10.1126/science.1211028openalex-snapshot
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
inferredcites →https://doi.org/10.1126/science.1621096openalex-snapshot
Evidence that eukaryotes and eocyte prokaryotes are immediate relatives
inferredcites →https://doi.org/10.1186/1471-2148-5-2openalex-snapshot
Rooting a phylogenetic tree with nonreversible substitution models
inferredcites →https://doi.org/10.1186/s12859-021-03956-5openalex-snapshot
Root Digger: a root placement program for phylogenetic trees
inferredcites →https://doi.org/10.1214/ss/1063994979openalex-snapshot
Bootstrapping Phylogenetic Trees: Theory and Methods
inferredcites →https://doi.org/10.1371/currents.rrn1212openalex-snapshot
A time-calibrated species-level phylogeny of bats (Chiroptera, Mammalia)
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pone.0182238openalex-snapshot
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
inferredcites →https://doi.org/10.1515/9783111385068-009openalex-snapshot
Prokaryote evolution and the symbiotic origin of eukaryotes
inferredcites →https://doi.org/10.1515/sagmb-2013-0077openalex-snapshot
Bayesian modelling of compositional heterogeneity in molecular phylogenetics
inferredcites →https://doi.org/10.3161/15081109acc2018.20.2.003openalex-snapshot
Parallel Amino Acid Deletions of Prestin Protein in Two Dramatically Divergent Bat Lineages Suggest the Complexity of the Evolution of Echolocation in Bats
inferredcites →https://doi.org/10.3161/15081109acc2019.21.1.005openalex-snapshot
Hypophysis Size Evolution in Chiroptera
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Extreme genome diversity and cryptic speciation in a harmful algal-bloom-forming eukaryote
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