Draft:StarBeast
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Submission declined on 7 August 2026 by Zippybonzo (talk). This draft reads like an advertisement. Wikipedia is an encyclopedia, not a platform for promotion or marketing. Drafts that are exclusively promotional may be deleted without notice.
Declined by Zippybonzo 57 days ago.Wikipedia articles must be written neutrally in a formal, impersonal, and dispassionate way. They should not read like a blog post, advertisement, or fan page. Rewrite the draft to remove:
Instead, only summarize in your own words a range of independent, reliable, published sources that discuss the subject. If you have a conflict of interest (e.g. you are the subject, an employee, or a relative) or are being paid to edit, you must disclose this to comply with Wikipedia's Terms of Use. | |
Submission declined on 6 August 2026 by WeirdNAnnoyed (talk). This draft appears to contain text generated by a large language model (such as ChatGPT). You cannot use LLMs to generate, draft, or rewrite article content.
Please delete the portions which were LLM-generated, and summarize in your own words a range of independent, reliable, published sources that discuss the subject. If you have used an LLM but you believe that your use is covered by one of the two exceptions (basic copyediting and translation between two languages in which you are fully fluent), please provide a transcript of the prompt(s) you used while writing your draft (see the how-to guide). Reviewers can make mistakes. If you have not received any LLM assistance, you may seek a second opinion at the AfC Help Desk. See the advice page on large language models for more information.This draft reads like an advertisement. Wikipedia is an encyclopedia, not a platform for promotion or marketing. Drafts that are exclusively promotional may be deleted without notice.
Declined by WeirdNAnnoyed 58 days ago.Wikipedia articles must be written neutrally in a formal, impersonal, and dispassionate way. They should not read like a blog post, advertisement, or fan page. Rewrite the draft to remove:
Instead, only summarize in your own words a range of independent, reliable, published sources that discuss the subject. If you have a conflict of interest (e.g. you are the subject, an employee, or a relative) or are being paid to edit, you must disclose this to comply with Wikipedia's Terms of Use. | |
This draft's references do not show that the subject meets Wikipedia's criteria for inclusion. The draft requires multiple published secondary sources that:
Declined by Sulfurboy 2 months ago.
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Comment: I think the sourcing is enough for notability, but there are some WP:PROMO issues with the text ("Integration with the wider BEAST2 ecosystem," the whole first paragraph of "Reception and use," etc.) Please rewrite in a more neutral manner. I also suspect some AI use, based on formatting, but I'm less certain about that. WeirdNAnnoyed (talk) 23:30, 6 August 2026 (UTC)
| StarBEAST | |
|---|---|
| Developers | Joseph Heled, Alexei Drummond, Huw Ogilvie, Remco Bouckaert, Jordan Douglas and others |
| Release | 2010 |
| Stable release | StarBeast3
|
| Written in | Java |
| Operating system | Cross-platform |
| Type | Bioinformatics, Phylogenetics |
| License | LGPL |
| Website | www |
StarBEAST (originally *BEAST and pronounced "star beast") is a Bayesian Markov chain Monte Carlo (MCMC) method and software package for the joint estimation of species trees, gene trees, divergence times and ancestral effective population sizes from multilocus molecular sequence data, under the multispecies coalescent (MSC) model. It is implemented as part of the BEAST platform for Bayesian evolutionary analysis. By modelling the coalescent process within a species tree, StarBEAST accounts for incomplete lineage sorting and the resulting discordance between individual gene trees, a source of error not addressed by the concatenation of loci.[1] It is a full-likelihood implementation of the multispecies coalescent.[2][3]
Since its introduction, the method has been reimplemented and extended through three major versions: the original *BEAST (2010), StarBEAST2 (2017) and StarBeast3 (2022).
Background
[edit]Species that have diverged recently often share ancestral genetic polymorphisms that sort independently in different parts of the genome, so that the evolutionary tree estimated from any single gene may differ from the true species tree. This phenomenon, known as incomplete lineage sorting, means that a species tree cannot in general be recovered reliably by concatenating multiple loci and analysing them as a single alignment; concatenation can be statistically inconsistent under high levels of incomplete lineage sorting, converging on an incorrect tree with strong support.[4] The multispecies coalescent model addresses this by treating each gene tree as an outcome of the coalescent process running backwards in time within the branches of a shared species tree, with the rate of coalescence governed by the effective population size on each branch.[1] Full-likelihood multispecies-coalescent methods remain statistically consistent under these conditions but are computationally expensive relative to concatenation and summary methods.[2][4]
StarBEAST performs Bayesian inference of the species tree and its parameters by jointly estimating the embedded gene trees, integrating over the uncertainty in each.[1]
Versions
[edit]*BEAST (2010)
[edit]The original method, *BEAST, was described by Joseph Heled and Alexei Drummond in 2010 and implemented within BEAST 1. It provided a full Bayesian framework that jointly infers the species tree topology, divergence times, population sizes and gene trees from multiple genes sampled from multiple individuals across a set of closely related species. A birth–death or Yule prior is placed on the species tree, and a multispecies coalescent prior links the gene trees to it.[1]
StarBEAST2 (2017)
[edit]StarBEAST2, published by Huw A. Ogilvie, Remco R. Bouckaert and Alexei J. Drummond in 2017, is a package for BEAST 2. It revised the model and MCMC operators, reporting speed-ups of roughly 13.5× and 13.8× on two empirical data sets and an average of about 33.1× across 30 simulated data sets relative to *BEAST. StarBEAST2 added MSC-aware relaxed molecular clock models for estimating per-species substitution rates alongside the species tree. StarBEAST2 also analytically integrates over the ancestral effective population sizes by default, marginalizing these parameters rather than sampling them explicitly.[5]
StarBeast3 (2022)
[edit]StarBeast3, published by Jordan Douglas, Cinthy L. Jiménez-Silva and Remco Bouckaert in 2022, is a further BEAST 2 package designed for large data sets. It introduced new MCMC proposals and an adaptive, parallelised inference scheme in which conditionally independent gene trees and their site models can be updated across multiple threads. The authors reported that StarBeast3 is faster than StarBEAST2 and *BEAST, on data sets of several hundred loci with relaxed-clock dating.[6]
See also
[edit]References
[edit]- 1 2 3 4 Heled, Joseph; Drummond, Alexei J. (2010). "Bayesian Inference of Species Trees from Multilocus Data". Molecular Biology and Evolution. 27 (3): 570–580. doi:10.1093/molbev/msp274. PMID 19906723.
- 1 2 Rannala, Bruce; Edwards, Scott V.; Leaché, Adam D.; Yang, Ziheng (2020). "The Multispecies Coalescent Model and Species Tree Inference". In Scornavacca, Céline; Delsuc, Frédéric; Galtier, Nicolas (eds.). Phylogenetics in the Genomic Era. pp. 3.3:1–3.3:21.
- ↑ Jiao, Xiyun; Flouri, Tomáš; Yang, Ziheng (2021). "Multispecies coalescent and its applications to infer species phylogenies and cross-species gene flow". National Science Review. 8 (12) nwab127. doi:10.1093/nsr/nwab127.
- 1 2 Liu, Liang; Wu, Shaoyuan; Yu, Lili (2015). "Coalescent methods for estimating species trees from phylogenomic data". Journal of Systematics and Evolution. 53 (5): 380–390. doi:10.1111/jse.12160.
- ↑ Ogilvie, Huw A.; Bouckaert, Remco R.; Drummond, Alexei J. (2017). "StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates". Molecular Biology and Evolution. 34 (8): 2101–2114. doi:10.1093/molbev/msx126. PMC 5850801. PMID 28431121.
- ↑ Douglas, Jordan; Jiménez-Silva, Cinthy L.; Bouckaert, Remco (2022). "StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent". Systematic Biology. 71 (4): 901–916. doi:10.1093/sysbio/syac010.
External links
[edit]| Relevant fields | ||
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| Basic concepts | ||
| Inference methods | ||
| Current topics | ||
| Group traits | ||
| Group types | ||
| Nomenclature | ||
Category:Bioinformatics software Category:Phylogenetics software Category:Computational phylogenetics Category:Free science software
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