An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis

D Jacob Machado, F Portella de Luna Marques… - …, 2022 - Wiley Online Library
… to both standard frequentist and Bayesian paradigms, as well … A review of recent phylogenetic
publications gives an idea of … provide empirical comparisons of these measures of support …

Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability

JM Chang, EW Floden, J Herrero, O Gascuel… - …, 2021 - academic.oup.com
… In comparison, there could be low bootstrap by individual … better than standard bootstrap
support measures and is useful both … phylogenetic trees confidence using maximum likelihood. …

[HTML][HTML] How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error

A Magee, M Karcher, FA Matsen IV, VM Minin - Bayesian analysis, 2024 - ncbi.nlm.nih.gov
… Next, we review background information on the ESS of one-dimensional Euclidean random
… for both Bayesian and maximum likelihood inference (where it summarizes bootstrap support…

An evolving view of phylogenetic support

C Simon - Systematic Biology, 2022 - academic.oup.com
… Here, I present a timeline and review significant events in the … analyses and PP were higher
numbers than bootstrap … renewed interest in maximum likelihood methods and improvement …

The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches

F Lemoine, O Gascuel - bioRxiv, 2024 - biorxiv.org
… a (which was not certified by peer review) is the author/funder, … We compare the results of
the two approaches on simulated … will mainly use the maximum likelihood framework, but the …

A machine-learning-based alternative to phylogenetic bootstrap

N Ecker, D Huchon, Y Mansour, I Mayrose… - …, 2024 - academic.oup.com
… the reliability of individual clades in an inferred phylogenetic … In comparison to parametric
tests in maximumlikelihood trees … Comparison of Bayesian and maximum likelihood bootstrap

Estimating phylogenies from shape and similar multidimensional data: why it is not reliable

C Varón-González, S Whelan… - Systematic …, 2020 - academic.oup.com
… (in those series where maximum likelihood performed better), … focus on the reliability of
estimated phylogenies in response … this study: based on the comparisons, it is very unlikely that a …

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

JA Fuentes-G, PD Polly, EP Martins - Evolution, 2020 - academic.oup.com
… its credibility through the 95% HDI. As a confirmatory procedure, we … maximum likelihood
and Bayesian approaches provide consistent results by giving more relevance to phylogenetic

Confidence intervals in molecular dating by maximum likelihood

E Paradis, S Claramunt, J Brown, K Schliep - Molecular Phylogenetics and …, 2023 - Elsevier
… This paper describes three bootstrap methods to infer … Bayesian inference are generally
in very good agreement, although they apparently did not compare confidence and credibility

Felsenstein phylogenetic likelihood

D Posada, KA Crandall - Journal of molecular evolution, 2021 - Springer
… with a sound statistical basis that this result is not very reliable. … Bayesian approaches, are
very popular in phylogenetics … using the standard log likelihood ratio test, comparing to a chi-…