The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
Abstract
Summary.We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees close to the current tree in the chain. We illustrate the algorithm with restriction site data on 9 plant species, then extend to DNA sequences from 32 species of fish. The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context
Huelsenbeck, J. P., & Rannala, B. (1997) · Science · doi:10.1126/science.276.5310.227 · Cited by 781
Statistical tests of models of DNA substitution
Goldman, N. (1993) · Journal of Molecular Evolution · doi:10.1007/bf00166252 · Cited by 736
Cited by
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 27,843
Self-citationMRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,806
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159
““coda” (Plummer et al. 2006) provides some of the functionality of Tracer within the R programming environment, while “AWTY” (Nylander the convergence of the phylogenetic tree parameter itself across multiple MCMC runs.”
MethodInfluentialPosada, D., & Buckley, T. R. (2004) · Systematic Biology · doi:10.1080/10635150490522304 · Cited by 3,927
Metadata
- Authors
- Mau, B., Newton, M. A., & Larget, B.
- Venue
- Biometrics
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-03
- Volume
- 55
- Issue
- 1
- Pages
- 1-12
- ISSN
- 0006-341X (ISSN-L)
- 1541-0420
- OpenAlex
- W2057293816
- Cited by
- 541
- References
- 5
- FWCI
- 25.70
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods. https://app.cochat.ai/papers/10.1111/j.0006-341x.1999.00001.x
- The paper
- Mau, B., Newton, M. A., & Larget, B. (1999). Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods. Biometrics. https://doi.org/10.1111/j.0006-341x.1999.00001.x
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
