HyPhy Methods & Analyses#

Explore the statistical methods, models, and workflows implemented in HyPhy:

• General Overview: Background on the standard MG94xREV substitution model and synonymous rate variation.
• Selection Analyses Overview: Detailed guides on MEME, FEL, FUBAR, BUSTED, aBSREL, RELAX, GARD, PRIME, and Contrast-FEL.
• Standard & Stand-alone Analyses: A complete directory of built-in CLI analyses, community batch files (hyphy-analyses), and the Galaxy integration ecosystem.
• Evolutionary Hypothesis Testing: Details on custom evolutionary testing pipelines.
• FitMultiModel: Details on fitting multiple instantaneous nucleotide changes.