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 …
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
… 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. …
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
… 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…
… 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 …
numbers than bootstrap … renewed interest in maximum likelihood methods and improvement …
The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches
… a (which was not certified by peer review) is the author/funder, … We compare the results of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 …
the two approaches on simulated … will mainly use the maximum likelihood framework, but the …
A machine-learning-based alternative to phylogenetic bootstrap
… the reliability of individual clades in an inferred phylogenetic … In comparison to parametric
tests in maximumlikelihood trees … Comparison of Bayesian and maximum likelihood bootstrap …
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 …
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 …
and Bayesian approaches provide consistent results by giving more relevance to phylogenetic …
Confidence intervals in molecular dating by maximum likelihood
… 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 …
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-…
very popular in phylogenetics … using the standard log likelihood ratio test, comparing to a chi-…