NJML: A hybrid algorithm for the neighbor-joining and maximum-likelihood methods

Molecular Biology and Evolution

Volumn 17, Issue 9, 2000, Pages 1401-1409

  Ota, Satoshi ^a   Li, Wen Hsiung ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Greedy algorithm; Phylogenetic reconstruction; Subtrees; Topology search

Indexed keywords

ALGORITHM; ARTICLE; HUMAN; MAXIMUM LIKELIHOOD METHOD; MOLECULAR GENETICS; PHYLOGENY; TAXONOMY;

EID: 0033857959     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026423     Document Type: Article

References (35)

1. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood
2. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction
3. Phylogenetic analysis: Models and estimation procedures
4. Evolutionary trees from DNA sequences: A maximum likelihood approach
5. Confidence limits on phylogenies: An approach using the bootstrap
6. A graph theoretic approach to the development of minimal phylogenetic trees
7. Robustness of maximum likelihood tree estimation against different patterns of base substitutions
8. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
9. Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny
10. On the maximum likelihood method in molecular phylogenetics
11. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
12. An empirical test of boot-strapping as a method for assessing confidence in phylogenetic analysis
13. The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
14. Evolution of protein molecules
15. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
16. Converting distance to time: Application to human evolution
17. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
18. A new version of the RDP (Ribosomal Database Project)
19. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small
20. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
21. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
22. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree
23. The neighbor-joining method: A new method for reconstructing phylogenetic trees
24. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
25. Bayesian probabilities and quartet puzzling
26. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
27. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
28. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock
29. Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique