Lecture slides

Below are the lecture slides for the course "Selection in Genes" that ran in 2022 in Lund, Sweden, by Prof Dr Maria Anisimova and Dr Jūlija Pečerska from ZHAW, Zürich, Switzerland.

• Markov Models of Sequence Evolution
• Hypothesis Testing and Model Selection
• Phylogenetic Inference
• Natural Selection and Codon Models
• Modelling Variability of Selection
• Site Models, Detecting Residues under Selection
• Detecting Episodic Positive Selection
• Pipelining for Large-Scale Analyses

Tutorials

• Parameter Estimation in PhyML
• Model Selection in PhyML
• ML Tree Inference in PhyML
• One Ratio Model Inference in PAML
• Branch Models in PAML
• Site Models in PAML
• Branch-site Model Inference in PAML
• Pipelining

Software

The software below will be used for the exercises.

• PhyML: PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework (download).
• PAML: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood (download).
• FigTree: FigTree is a graphical viewer of phylogenetic trees (download).
• AliView: AliView is an alignment viewer and editor (download).