Tutorials

A collection of tutorials on phylogenomic and related analyses, written for analyses on the lynx server at LMU Munich.

Prepration

• Requirements
  A list of all installations required for the tutorials

• Getting Started
  General instructions on the use of these tutorials

Phylogenetic Inference

• Maximum-Likelihood Phylogenetic Inference
  A tutorial on maximum-likelihhood phylogenetic inference

• Bayesian Phylogenetic Inference
  A tutorial on Bayesian inference of time-calibrated phylogenies

Species-tree Inference

• 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

Whole-genome Alignment

• Whole-Genome Alignment
  A tutorial on repeat masking and whole-genome alignment of assembled genomes

Phylogenetic inference with SNPs

• 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

Species-network Inference

• Maximum-Likelihood Inference of Species Networks
  A tutorial on maximum-likelihood phylogenetic inference of species networks

Introgression Detection

• Analysis of Introgression with SNP Data
  A tutorial on the analysis of hybridization and introgression with SNP data

Species Delimitation

• Bayes Factor Species Delimitation with SNP Data
  A tutorial on Bayes factor species delimitation with SNP data

Simulation-based Inference

• Inference from Simulated Data
  A tutorial on coalescent simulations of genomic data and inferences from simulated data