Datamonkey Documentation
Datamonkey is a free, public web application for evolutionary sequence analysis, powered by HyPhy. It provides a suite of methods for detecting natural selection, recombination, and other evolutionary processes from coding sequence alignments.
Guide
- Analyzing Data — submitting jobs, interpreting results
- Data Files — accepted input formats and requirements
- Local Installation — running HyPhy locally
- About
Methods
- General Information — overview and how to choose a method
- aBSREL — adaptive branch-site test for episodic diversification
- B-STILL — Bayesian test for invariant sites
- BGM — Bayesian graphical models for coevolving sites
- BUSTED — branch-site unrestricted statistical test for episodic diversification
- Contrast-FEL — test for differences in selective pressures between groups
- FADE — FUBAR approach to directional evolution
- FEL — fixed effects likelihood for site-wise dN/dS estimation
- FUBAR — fast unconstrained Bayesian approximation
- GARD — genetic algorithm for recombination detection
- MEME — mixed effects model of evolution for episodic selection
- MSS — multiple synonymous substitution models
- MULTI-HIT — accounting for multiple simultaneous substitutions
- NRM — nucleotide rate matrix analysis
- PRIME — property-informed models of evolution
- RELAX — test for relaxation or intensification of selection
- SLAC — single-likelihood ancestor counting
Resources
