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Tutorials on phylogenetic and phylogenomic inference

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# Tutorials

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 These tutorials were written for a Physalia workshop in 2019 and are no longer updated. The content may therefore be rather outdated.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be found on [https://github.com/ForBioPhylogenomics](https://github.com/ForBioPhylogenomics); however, also these are no longer updated.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](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](https://www.bio.lmu.de/en/research/research-fields/zoology/matschiner-lab/) and students of their courses have access.
 
## Preparation

* [Requirements](requirements.md) A list of all installations required for the tutorials

* [Getting Started](getting_started.md) General instructions on the use of these tutorials

## Phylogenetic inference

* [Multiple Sequence Alignment](multiple_sequence_alignment/README.md) A tutorial on multiple sequence alignment

* [Substitution Model Selection](substitution_model_selection/README.md) A tutorial on the selection of a substitution model for phylogenetic analysis

* [Maximum-Likelihood Phylogenetic Inference](ml_phylogeny_inference/README.md) A tutorial on phylogenetic inference with maximum likelihood

* [Bayesian Phylogenetic Inference](bayesian_phylogeny_inference/README.md) A tutorial on Bayesian inference of time-calibrated phylogenies

* [Phylogenetic Divergence-Time Estimation](divergence_time_estimation/README.md) A tutorial on phylogenetic divergence-time estimation with with fossils

## Species-tree inference

* [Ortholog Detection](ortholog_detection/README.md) A tutorial on the detection of orthologs in assembled genomes

* [Maximum-Likelihood Species-Tree Inference](ml_species_tree_inference/README.md) A tutorial on maximum-likelihood species-tree inference based on gene trees

* [Bayesian Species-Tree Inference](bayesian_species_tree_inference/README.md) A tutorial on Bayesian inference of time-calibrated species trees

* [Local Assembly](local_assembly/README.md) A tutorial on the assembly of individual marker sequences from short reads

* [Species-Tree Inference with SNP Data](species_tree_inference_with_snp_data/README.md) A tutorial on the inference of species trees from SNP data based on quartets

* [Divergence-Time Estimation with SNP Data](divergence_time_estimation_with_snp_data/README.md) A tutorial on Bayesian divergence-time estimation with SNP data

## Phylogenomic analyses of introgression

* [Bayesian Analysis of Species Networks](bayesian_analysis_of_species_networks/README.md) A tutorial on Bayesian phylogenetic analysis of species networks

* [Analysis of Introgression with SNP Data](analysis_of_introgression_with_snp_data/README.md) A tutorial on the analysis of hybridization and introgression with SNP data

* [Analysis of Introgression with Chromosome-Length Alignments](analysis_of_introgression_with_chromosome_length_alignments/README.md) A tutorial on the analysis of hybridization and introgression with whole-chromosome alignments

## Ancestral-recombination-graph inference

* [Genome-Wide Genealogy Estimation With SNP Data](genome_wide_genealogy_estimation_with_snp_data/README.md) A tutorial on the inference and analysis of genome-wide genealogies through ancestral recombination graphs.

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