Tutorials

April 12, 2026 · View on GitHub

A collection of tutorials on phylogenetic and phylogenomic analyses

Note

These tutorials were written for a Physalia workshop in 2019 and are no longer updated. The content may therefore be rather outdated. Slightly newer versions of these tutorials can be found on https://github.com/ForBioPhylogenomics; however, also these are no longer updated. The only updated versions of (some of) these tutorials can be found on https://github.com/mmatschiner/lynx, but those are written specifically for analyses on the lynx server at LMU Munich, to which only members of the LMU Systematic Zoology group and students of their courses have access.

Preparation

Requirements
A list of all installations required for the tutorials
Getting Started
General instructions on the use of these tutorials

Phylogenetic inference

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

Species-tree inference

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

Phylogenomic analyses of introgression

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

Ancestral-recombination-graph inference

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