Tutorials

A collection of tutorials on phylogenetic and phylogenomic analyses

Preparation

Multiple Sequence Alignment A tutorial on multiple sequence alignment
Substitution Model Selection A tutorial on the selection of a substitution model for phylogenetic analysis
Maximum-Likelihood Phylogenetic Inference A tutorial on phylogenetic inference with maximum likelihood
Bayesian Phylogenetic Inference A tutorial on Bayesian inference of time-calibrated phylogenies
Phylogenetic Divergence-Time Estimation A tutorial on phylogenetic divergence-time estimation with with fossils

Ortholog Detection A tutorial on the detection of orthologs in assembled genomes
Maximum-Likelihood Species-Tree Inference A tutorial on maximum-likelihood species-tree inference based on gene trees
Bayesian Species-Tree Inference A tutorial on Bayesian inference of time-calibrated species trees
Local Assembly A tutorial on the assembly of individual marker sequences from short reads
Species-Tree Inference with SNP Data A tutorial on the inference of species trees from SNP data based on quartets
Divergence-Time Estimation with SNP Data A tutorial on Bayesian divergence-time estimation with SNP data

Bayesian Analysis of Species Networks A tutorial on Bayesian phylogenetic analysis of species networks
Analysis of Introgression with SNP Data A tutorial on the analysis of hybridization and introgression with SNP data
Analysis of Introgression with Chromosome-Length Alignments A tutorial on the analysis of hybridization and introgression with whole-chromosome alignments

Genome-Wide Genealogy Estimation With SNP Data A tutorial on the inference and analysis of genome-wide genealogies through ancestral recombination graphs.