Detecting Selection in Genes

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

PhyML v3.3.2050429 Tutorials

Parameter Estimation
Model Selection
ML Tree Inference

CodeML Tutorials

One Ratio Model Inference
Branch Model Inference
Site Model Inference
Branch-site Model Inference
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).