AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
Clicks: 3
ID: 291392
2007
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This
article has not been analysed, so there is no overall score —
reader engagement is measured and shown alongside.
Reader Engagement
Emerging Content
0.6
/100
3 views
2 readers
AI Quality Assessment
Not analyzed
Readership in this journal
EmergingRanked #727 of 835 articles by views in BMC Bioinformatics
Most read
Least read
Bar heights use a square-root scale. Only the 120 most-read articles are drawn; the journal has 835 in total.
Mint this article as an NFT
Not yet mintedCreate a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.
5
SUSD
one-off · no wallet required
Abstract
A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation.The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.
| Reference Key |
openalex_W2128841626
Use this key to autocite in the manuscript while using
SciMatic Manuscript Manager or Thesis Manager
|
|---|---|
| Authors | Johan A. A. Nylander, James C. Wilgenbusch, Dan L. Warren, David L. Swofford |
| Journal | BMC Bioinformatics |
| Year | 2007 |
| DOI |
10.1093/bioinformatics/btm388
|
| URL | |
| Keywords | Keywords not found |
Citations
No citations found. To add a citation, contact the admin at info@scimatic.org
Comments
No comments yet. Be the first to comment on this article.