Prospects for inferring very large phylogenies by using the neighbor-joining method.
Explore this paper's citation graph
Summary
The simulation results show that the accuracy of NJ trees decline only by approximately 5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio.
- Type
- article
- Published
- 2004-07-27
- Cited by
- 5,607
- References
- 41
- Access
- Open access
- OpenAlex
- https://openalex.org/W2121677860
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:13852368
Keywords
Tree (set theory), Transversion, Pairwise comparison, Substitution (logic), Inference
References
- Unbiased estimation of evolutionary distance between nucleotide sequences.
- Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases.
- Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used.
- Computational analysis of evolution and conservation in a protein superfamily.
- A stepwise algorithm for finding minimum evolution trees.
- A rapid heuristic algorithm for finding minimum evolution trees.
- The Use of Tree Comparison Metrics
- Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
- The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small.
- Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting.
- Incomplete taxon sampling is not a problem for phylogenetic inference
- Comparison of phylogenetic trees
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
- When is it safe to use an oversimplified substitution model in tree-making?
- Analysis of animal movement using opportunistic individual identifications: application to sperm whales
- The neighbor-joining method: a new method for reconstructing phylogenetic trees.
- Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference.
- Phylogenetic analysis in molecular evolutionary genetics.
- Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands
- Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle
Cited by
- Taxonomic and phylogenetic study of rust fungi forming aecia on Berberis spp. in Sweden
- Application of biocathode in microbial fuel cells: cell performance and microbial community
- Pathogenomics of the Virulence Plasmids of Escherichia coli
- Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping
- The aconitate hydratase family from Citrus
- A distance-based least-square method for dating speciation events.
- Comparison of volatile blends and gene sequences of two isolates of Metarhizium anisopliae of different virulence and repellency toward the termite Macrotermes michaelseni
- Characterization of a porin channel in the endosymbiont of the trypanosomatid protozoan Crithidia deanei.
- Cytochrome c oxidase subunit I barcoding of the green bee-eater (Merops orientalis).
- Short communication: analysis of the integrase gene from HIV type 1-positive patients living in a rural area of West Cameroon.
- Plasmodium vivax apicoplast genome: a comparative analysis of major genes from Indian field isolates.
- Molecular relationship between field and vaccine strain of measles virus and its persistence in Pakistan
- Positive selection for gains of N-linked glycosylation sites in hemagglutinin during evolution of H3N2 human influenza A virus.
- Evidence of interspecies O antigen gene cluster transfer between Shigella boydii 15 and Escherichia fergusonii
- An O-Acetylserine (thiol) Lyase from Leucaena leucocephala Is a Cysteine Synthase But Not a Mimosine Synthase
- Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering
- Identification of a natural recombination in the F and H genes of feline morbillivirus.
- IDENTIFICATION OF A NOVEL INTERTYPIC RECOMBINANT SPECIES D HUMAN ADENOVIRUS IN A PEDIATRIC STEM CELL TRANSPLANT RECIPIENT
- Ecology and Biotechnology of Selenium-Respiring Bacteria
- Exploring ComQXPA quorum-sensing diversity and biocontrol potential of Bacillus spp. isolates from tomato rhizoplane
Related papers
- The specificity of base-pair substitution induced by the mutL and mutS mutators in E. coli.
- Transversion-specific purine analogue mutagens and the mechanism of hydroxylaminopurine mutagenesis.
- Benzo[a]pyrene‐induced mutagenesis of p53 hot‐spot codons 248 and 249 in human hepatocytes
- Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence.
- Enhanced characterization of the thyA system for mutational analysis in Escherichia coli: Defining mutationally "hot" regions of the gene.
- beta-lactamase gene promoters of 71 clinical strains of Klebsiella oxytoca
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences