What is bootstrapping in phylogenetics and how should bootstrap values be interpreted?

Bootstrapping in phylogenetics assesses the statistical support for branches in a phylogenetic tree. The process: 1) Resample alignment columns with replacement to create pseudo-replicates of the same size. 2) Build a tree from each bootstrap replicate (typically 100-1000 replicates). 3) Calculate bootstrap support - percentage of replicate trees containing each clade. Interpretation: >90% strong support, 70-90% moderate support, <70% weak support. Limitations: bootstrap values are measures of repeatability, not accuracy; can be inflated with many sites; don't indicate if the correct tree was found. Alternatives include Bayesian posterior probabilities (which measure probability of clade) and SH-aLRT support values (faster approximation).