Topic outline

  • General

    Introduction to Markov models

    Lausanne, 12-14 April 2016


    Markov models play an important role in biological modelling. They are involved in many areas of biology including gene and motif predictions to phylogenetics and macroevolution. The goal of this course is to give a broad theoretical overview of these models and the biological processes that can be studied with them.

    Learning objectives

    At the end of the course, you will be supposed to know:

    i) theoretical background on Markov models,

    ii) Basic concepts for Markov chain Monte Carlo,

    iii) Maximum likelhood estimation of Markov model parameters for sequence evolution,

    iv) Hidden Markov models


    Knowledge: Good understanding of mathematics for biologist; knowledge of evolutionary biology; ability to use R.

    Computer: bring your own laptop

    Software: R installed

    Location & timing

    University of Lausanne, Genopode building, classroom 2020 (Metro M1 line, Sorge station). The course starts at 9:00 and ends around 17:00.

    Additional information

    For technical and scientific questions, please contact

    Link for registration

    • Programme

      Topic 1 (Day 1 morning)
      Introduction to Markov models
      Teacher: Sophie Hautphenne, Chair of Statistics, EPFL

      Topic 2 (Day 1 afternoon)
      Introduction to Markov chain Monte Carlo
      Teacher: Nicolas Salamin, Computational Phylogenetics, SIB / UNIL

      Topic 3 (Day 2)
      Markov models in phylogenetics and molecular evolution
      Teacher: Laurent Géguen, Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard, Lyon

      Find the course material here (TP_EvolMol) and here (TP_BPP).

      Topic 4 (Day 3)
      Hidden-Markov models
      Teacher: Daniel Wegmann, Statistical and Computational Evolutionary Biology Group, SIB / UNIFR