General information

Time table

Week 1

Date Time Topic Lecturer Slides
Mon, Feb 3, 2014 10:15 - 12:00 Introduction to phylogenetics Müller, Kai Power Point (10 MB) PDF slides (6 MB) PDF overview (3 MB)
13:00 - 17:00 Command line, batch files, introduction to sequence evolution Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
Tue, Feb 4, 2014 10:15 - 12:00 Sequencing methods Wicke, Susann Power Point (7 MB) PDF slides (3 MB) PDF overview (1 MB)
13:00 - 15:45 Sequence evolution, Phylogentic file types, Introduction into tree and alignment editors Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
16:00 - 17:00 IEB seminar  
Wed, Feb 5, 2014 10:15 - 12:00 Sequence databases Wicke, Susann Power Point (2 MB) PDF slides (2 MB) PDF overview (1 MB)
13:30 - 17:00 Trace file processing with PhyDE Wicke, Susann  
Thu, Feb 6, 2014 10:15 - 12:00 Mathematical basics Stöver, Ben Power Point (2 MB) PDF slides (1 MB) PDF overview (1 MB)
13:00 - 16:15 Obtaining data from sequence databases Wicke, Susann  
16:15 - 17:00 Presentation of the available seminar topics Stöver, Ben Wicke, Susann  
Fri, Feb 7, 2014 10:15 - 12:00 Substitution models, clustering methods Stöver, Ben Power Point (4 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 16:30 NJ exercise, distance methods with MEGA Stöver, Ben  
16:30 - 17:00 Assignment of of the seminar topics Stöver, Ben  

Week 2

Date Time Topic Lecturer Slides
Mon, Feb 10, 2014 10:15 - 12:00 Multiple sequence alignment Stöver, Ben Power Point (3 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 17:00 Needleman Wunsch exercise, comparison of MSA algorithms Stöver, Ben  
Tue, Feb 11, 2014 10:15 - 12:00 Maximum parsimony, tree searches, resampling plans Stöver, Ben Power Point (3 MB) PDF slides (1 MB) PDF overview (1 MB)
13:00 - 15:45 MP exercise, MP with MEGA Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
16:00 - 17:00 IEB seminar  
Wed, Feb 12, 2014 10:15 - 12:00 Morphological character reconstruction, Bremer support Greenwood, Jennifer PDF slides (17 MB)
13:00 - 17:00 Morphological character reconstruction, MP with TNT, resampling plans Greenwood, Jennifer Additional information
Thu, Feb 13, 2014 10:15 - 12:00 Maximum Likelihood Stöver, Ben Power Point (3 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 15:45 Maximum Likelihood with GARLI and RAxML Stöver, Ben  
16:00 - 17:00 IEB seminar  
Fri, Feb 14, 2014 IEB research day (no course)  

Week 3

Date Time Topic Lecturer Slides
Mon, Feb 17, 2014 10:15 - 12:00 Seminar Stöver, Ben Wicke, Susann  
13:00 - 16:00 Seminar Stöver, Ben Wicke, Susann  
Tue, Feb 18, 2014 10:15 - 12:00 Bayesian statistics, MCMC Stöver, Ben Power Point (3 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 15:45 Bayesian inference with MrBayes, storing and reading additional node data in phylogenetic file formats Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
16:00 - 17:00 IEB seminar  
Wed, Feb 19, 2014 10:15 - 12:00 Model- and hypothesis tests Wicke, Susann Power Point (2 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 13:30 Tree merging with TreeGraph 2 Stöver, Ben  
13:30 - 14:15 Seminar Stöver, Ben Wicke, Susann  
14:15 - 17:00 Model- and hypothesis tests with HyPhy, part 1 Wicke, Susann  
Thu, Feb 20, 2014 10:15 - 12:00 More realistic models, Topological tests Wicke, Susann  
13:00 - 16:30 Model- and hypothesis tests with HyPhy, part 2 Wicke, Susann  
16:30 - 17:00 Discussion of example questions for the exam Stöver, Ben Wicke, Susann  
Fri, Feb 21, 2014 11:00 - 12:30 Divergence age estimation Müller, Kai Power Point (2 MB) PDF slides (2 MB) PDF overview (1 MB)
13:30 - 17:00 Divergence age estimation with BEAST Müller, Kai  

Week 4

Date Time Topic Lecturer Slides
Mon, Feb 24, 2014 10:15 - 12:00 Basic principles of protein structure evolution Bitard Feildel, Tristan PDF slides (13 MB)
13:00 - 17:00 Basic principles of protein structure evolution Bitard Feildel, Tristan  
Tue, Feb 25, 2014 Time for preparation of the exam  
16:00 - 17:00 IEB seminar  
Wed, Feb 26, 2014 10:15 - 12:00 Opportunity to ask questions in preparation for the exam Stöver, Ben  
Time for preparation of the exam  
Thu, Feb 27, 2014 9:00 - 12:00 Exam  

Download example questions for the exam (1 MB).
Download solved example questions for the exam (1 MB).

Textbooks

See according lecture slides for relevent chapters of theses books.

Software

The following phylogenetic software will be used in the course.

Tree and alignment editors, multiple sequence alignment

Name License Description
TreeGraph 2 GNU General Public License Phylogenetic tree editor
FigTree free The tree editor of BEAST
phyDE Free, currently closed source Alignment editor
AlignmentComparator GNU General Public License Yet unpublished application from the bioinfweb project to compare alternative multiple sequence alignments
MSA algorithms free Different multiple sequence alignment algorithms provided by the EBI. (Clustal Omega, ClustalW2, DbClustal, Kalign, MAFFT, MUSCLE, MView, T-Coffee)
RandSeq for use in the course Little tool from this diploma thesis to generate random sequences.

See bioinfo.unice.fr/biodiv/Tree_editors.html or en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_softwarefore for more phylogenetic tree editors.

Maximum parsimony, distances, maximum likelihood, bayesian inference

Name License Description
MEGA free for use in research and education MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. (MEGA is installed on NWZNet machines.)
TNT free for personal use TNT (Tree analysis using New Technologies) is a program for phylogenetic analysis under parsimony. TNT incorporates fast tree-searching algorithms like Ratchet, sectorial searches, tree-drifting, and tree-fusing
PAUP* Proprietary Tools for inferring and interpreting phylogenetic trees. (PAUP* is installed on NWZNet machines.)
RAxML Open source Randomized Axelerated Maximum Likelihood
RAxML GUI Open source Graphical user interface for RAxML
GARLI Open source GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned sequence datasets using the maximum-likelihood criterion.
Mr. Bayes Open source Bayesian Inference of Phylogeny
PRAP 2 free Parsimony and likelihood ratchet analyses with PAUP*, Calculation of Bremer support
Leaphy free Likelihood estimation algorithms in phylogenetics (Needs cygwin to run under Windows.)

Ancestral character state reconstruction

Name License Description
Mesquite Open source Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
BayesTraits free BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.

Divergence age estimation

Name License Description
BEAST 2 free BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
Tracer free Used to analyze the output of BEAST

Model- and hypothesis tests, tree evaluation

Name License Description
jModelTest GNU General Public License jMODELTEST ijModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution.
ProtTest GNU General Public License PROTTEST (ModelTest's relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment).
ProtTest 3 free PROTTEST3 is a high-performance computing program for selecting the model of protein evolution that best fits a given set of aligned sequences.
HyPhy Open source Hypothesis testing using Phylogenies
PAML free for academic use only Phylogenetic Analysis by Maximum Likelihood
CONSEL Open source CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem.

Workflow manager

Name License Description
UGENE GNU General Public License 2 Workflow manager for bioinformatic tasks
Taverna Lesser General Public License (LGPL) Version 2.1 Taverna is an open source and domain-independent Workflow Management System ? a suite of tools used to design and execute scientific workflows and aid in silico experimentation.
Galaxy Academic Free License version 3.0 Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
Bioclipse Eclipse Public License (EPL) + exception Bioclipse is a free and open source workbench for the life sciences based on the Eclipse Rich Client Platform (RCP).

Pages that list additional phylogenetic software