Language: English
Instructors:
Prof. Dr. Dirk Metzler (lectures and exercises),
Dr. Ulrich Knief
(practical exercises on phylogenetics),
Dr. Ricardo Pereira
(practical exercises on population genetics)
Additional exercises/practicals for block courses Phylogenetics I/II and
Comp. Pop. Gen. I/II: Tuesday 9:00 to 12:00 taught by
Dr. Ulrich Knief
and Dr. Ricardo Pereira.
Note: times for the practicals population genetics taught by Ricardo Pereira
the exact time slots may be subject to change to avoid overlap with other courses.
Target group (Zielgruppe) and ECTS points:
Master's and PhD students in EES/MEME, Bioinformatics, Biostatistics, Biology, Mathematics, Statistics,...
Please find the module description for this course
in the official module catalog
of the bioinformatics master's program.
Students can obtain 8 ECTS for passing the exam of the entire course Computational Methods in Evolutionary Biology.
Students in block-structured programms like EES, MEME and the
Master's program in Biology can participate block-wisely.
For each block, combined with the additiona practical part,
students can obtain 3 ECTS by passing the exam and giving a presentation in the practical part.
General Introduction
Oct 20:
Structure of the course and some general remarks
(duration: 19:05 [Min:Sec])
Classical phylogenetics methods:
Oct 20: Phylogenetics lectures overview and notations
(26:22)
Oct 20: Distance-based phylogeny reconstruction with UPGA
(37:27)
Oct 20 or 22: Software: Simple phylogenetic analysis in R and how to use a Linux server
(46:53)
Oct 22: Distance-based phylogeny reconstruction with Neighbor Joining
(28:11)
Oct 22: Parsimony and how to calculate it for a given tree (and given data)
(17:31)
Oct 22: Searching for the most parsimonious tree
(44:30)
Oct 27: Difference measures for phylogenetic trees (14:34)
Oct 27: Software: PHYLIP
(33:58)
Maximum-Likelihood based methods:
The videos in this section will require some basics
from probability theory.
If you need a brief reminder to the basic terms of probability theory and the
law of total probability you can watch this video:
Basic concepts of probability theory (22:13)
Oct 27: Maximum-likelihood principle and Felsenstein's pruning algorithm (46:02)
Oct 27 or 29: Software: Seq-gen and a simulation study with phylip (43:06)
Oct 29: The Jukes-Cantor model of sequence evolution (49:25)
Oct 29: Markov chains and their equilibria (28:34)
Nov 3: Idea of proof of convergence of irreducible aperiodic Markov chains (13:36)
Nov 3: Reversibility of Markov chains (14:01)
Nov 3: Software: maximum-likelihood phylogeny reconstruction and bootstrapping with RAxML (27:36)
Nov 3: Searching for the maximum-likelihood phylogeny (29:34)
Nov 5: Insights from ML for parsimony and distance-based phylogeny (22:50)
Nov 5: Consistency of ML tree reconstruction (22:42)
Nov 5: Bootstrapping (34:14)
Bayesian sampling with MCMC:
Nov 10: Bayesian statistics and MCMC (47:03)
Nov 10: MCMCMC and Gibbs sampling (37:34)
Nov 10 or 12: Software: Bayesian phylogentic analysis with Beast (43:55)
Nov 12: Effective sample sizes in MCMC, problematic priors and mixtures of gene trees (30:31)
Common problems in phylogenetics and consequences for phylogenomics
Nov 12: long-branch attraction, recombination, incomplete lineage sorting, horizontal gene transfer (28:08)
Nov 12: gene families, orthologs, paralogs, xenologs and consequences for phylogenomics (22:58)
Models for substitution processes in sequence evolution:
Nov 17: Rate matrices (35:26)
Nov 17: Exponential waiting times for the next mutation (14:09)
Nov 17: Calculating transition matrices (may contain traces of linear algebra) (37:12)
Nov 19: Calculating transition matrices for continuous-time models (18:07)
Nov 19: F84: a model to avoid some matrix algebra (11:42)
Nov 19: Substitution-rate heterogeneity, relaxed-clock models and time-calibration using fossils (47:46)
Nov 19: Software: fossil-based time calibration with BEAST (20:59)
Quantitative traits and independent contrasts:
Nov 24: The Brownian motion model for (neutral) quantitative trait evolution and some basics on normally distributed vectors (48:42)
Nov 24: Reduced ML and Felsenstein's prunig algorithm for quantitative traits (44:41)
Nov 24: Software: phylip contrasts (8:25)
Model-selection strategies
Nov 26: Model selection (64:50)
Statistical Alignment
Nov 26 and Dec 1: Introduction to statistical alignment (69:40)
Dec 1: Statistical alignment with longer gaps (11:55)
Dec 1: Simultaneous sampling of phylogenies and alignments (48:15)
Statistical Tests for Phylogentic Trees (Extra material, not part of the course in WS 21/22)
The Kishino–Hasegawa Test (13:03)
The Shimodaira–Hasegawa Test (19:14)
The SOWH Test (10:41)
Anisimova and Gascuel's approximate likelihood-ratio test (23:25)
Introduction to basic models of population genetics
Dec 3: General remarks, Wright-Fisher model and Kingman's Coalescent (80:02)
Dec 8: Population-scale mutation rate θ, nucleotide diversity and Tajima's D (44:04)
Dec 8: Overview of coalescent-based parameter estimation approaches (27:18)
Dec 8 or 10: Software: Population genetic data simulation with ms and scrm and summary static calculations with R (44:26)
Likelihood-based inference with importance sampling and MCMC
Dec 10: Likelihoods in population genetics and the idea of importance sampling (49:14)
Dec 10: The importance sampling method of B. Griffiths and S. Tavaré (29:20)
Dec 15: LAMARC's approach of using MCMC for Importance Sampling (43:01)
Dec 15: Software: A simple LAMARC analysis (52:39)
Dec 15 or 17: MCMC sampling of genealogies (60:20)
Dec 17: Ancestral Recombination Graphs and some more aspects of MCMC sampling in LAMARC (40:32)
Dec 22: Software: How to simulate data for testing LAMARC (44:51)
Dec 22: MCMC methods for the isolation-migration model as implemented in IM/IMa/IMa2 (54:54)
Approximate Bayesian Computation (ABC) and other summary-statistics based methods
Jan 7: ABC with local regression and MCMC without likelihoods (77:35)
Jan 7: Software: an ABC analysis with the abc package in R (41:49)
Jan 12: Sequential/Adaptive ABC (ABC-PMC) (24:08)
Jan 12: Combining summary statistics with partial least squares (42:49)
Jan 14: Composite-likelihood approaches and the Joint site-frequency spectrum (58:40)
Sequential approximations of the ancestral recombination graph and HMMs
Jan 14: Sequential Markovian Coalescents (SMC) and other ARG approximations (24:20)
Jan 19: Applying HMMs: PSMC and MSMC (76:02)
Detecting population structure with programs like STRUCTURE
Jan 21: Method in STRUCTURE with and without admixture (77:24)
Jan 26: Software: getting started with STRUCTURE (19:20)
Jan 26: STRUCTURE model variants and alternative tools (56:38)
Selection: Models and statistics
Jan 28: Basic population genetic model of directional selection (33:53)
Jan 28: Weak selection and the ancestral selection graph (26:35)
Feb 2: Selective sweeps and how they are modeled in simulated in msms (43:18)
Feb 2: Statistics for detecting selective sweeps (33:34)
Feb 4: Soft sweeps, incomplete sweeps and population demography (41:21)
Feb 4: A statistic for detecting balancing selection (30:42)
Li and Stephens' PAC approach
Feb 9: Li and Stephens' PAC approach and its application to infer recombination and LD blocks (53:19)
Feb 9: PAC applied to inferring demography and selection (47:06)
Feb 11: Phasing (22:02)
Extra Material: The general expectation-maximization algorithm (26:27)
Feb 11: Phasing with PHASE, again applying PAC (40:26)
Announcement for bioinformaticians in official LMU course overview