ChronAeon Tutorials & Practitioner Guides

Step-by-step guides for calibrating molecular clocks, interpreting analytical Denny-Fieller confidence bounds, deconvolving multi-rate epidemic lineages, and migrating from traditional Bayesian MCMC (BEAST).

Tutorial 01 20 min read

Practical Molecular Clock Calibration & Emergence Dating

A comprehensive operational guide for computational virologists and epidemiologists. Covers sequence data hygiene, reading-frame verification, single-clock estimators (OLS and foundation PGLS), exact analytical Denny-Fieller confidence bounds, Leave-One-Out Cross-Validation (LOOCV), and a step-by-step worked example on the 2019 Cuban Zika virus epidemic.

Zero-imputation data hygiene & decimal date harmonization
Attention PGLS with exact REML Pagel's λ optimization
Analytical Fieller intervals ($g$-ratio bounding)
Spectral AutoClock multi-rate deconvolution

Read Web Tutorial → Download .md ↓

Tutorial 02 25 min read

ChronAeon for BEAST Users: The Rosetta Stone

A translation guide for Bayesian phylogeneticists moving from BEAUti, BEAST 1.x/2.x, and Tracer into ChronAeon's geometric framework. Maps demographic priors, Tracer ESS, relaxed clocks (UCLN), and trace diagnostics to their analytical geometric equivalents, featuring direct ingestion of native beast.xml.gz files and a worked comparison on Dengue Virus Type 4.

Rosetta stone translation table (BEAST ↔ ChronAeon)
Direct ingestion of native beast.xml.gz without conversion
From Tracer ESS to Denny-Fieller diagnostics
Scaling comparison: 3,200x speedup on 1,600 Ebola genomes

Read Web Tutorial → Download .md ↓

Quick CLI Reference

1. Date Directly from Compressed BEAST XML

chronaeon date --beast dataset.xml.gz --loocv

2. Date from In-Frame FASTA & Dates CSV

chronaeon date -a alignment.fasta -d dates.csv --loocv

3. AutoClock Multi-Rate Lineage Deconvolution

chronaeon autoclock --beast dataset.xml.gz

4. Generate Publication-Grade Diagnostic Figures

chronaeon date --beast dataset.xml.gz --plot