Jafarighm/phylogeny

Tutorials on phylogenetic and phylogenomic inference

Tutorials

A collection of tutorials on phylogenetic and phylogenomic analyses

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.