The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML).
The paper: M.C. Brandley et al., "Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards," Systematic Biol, 54:373-90, 2005. (Cited in 73 papers) The ...