A collection of tutorials on phylogenetic and phylogenomic analyses
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Requirements
A list of all installations required for the tutorials -
Getting Started
General instructions on the use of these tutorials
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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
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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
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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.