General information

  • The lecture takes place daily from 10:15 to 12:00, the practical from 13:00 to 17:00. The practical is optional for computer science students.
  • Start of the course: Mon, Feb 2, 2015, 10 c.t.
  • Room: Lecture and practical take place in the COM-LAB B (SP2 23, Schlossplatz 2b, Building 0352).

Time table

Week 1

Date Time Topic Lecturer Slides
Mon, Feb 2, 2015 10:15 - 12:00 Introduction to phylogenetics Wicke, Susann PDF slides (8 MB)
13:00 - 15:30 Command line, batch files, introduction to sequence evolution Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
15:30 - 18:00 Seminar preparation  
Tue, Feb 3, 2015 10:15 - 12:00 Sequencing methods, trace file processing Wicke, Susann PDF slides (3 MB)
13:00 - 15:45 Sequence databases Wicke, Susann  
16:00 - 17:00 IEB seminar  
Wed, Feb 4, 2015 10:15 - 12:00 Mathematical basics Stöver, Ben Power Point (2 MB) PDF slides (1 MB) PDF overview (1 MB)
13:30 - 15:30 Alignment and tree editors, phylogenetic file formats and ontologies Stöver, Ben  
15:30 - 18:00 Seminar preparation  
Thu, Feb 5, 2015 10:15 - 12:00 Substitution models, clustering methods Stöver, Ben Power Point (4 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 15:30 Distance methods exercise, distance methods in MEGA Stöver, Ben  
15:30 - 18:00 Seminar preparation  
Fri, Feb 6, 2015 10:15 - 12:00 Seminar preparation  
12:00 - 13:45 Multiple sequence alignment (lecture at different time) Stöver, Ben Power Point (3 MB) PDF slides (2 MB) PDF overview (1 MB)
14:45 - 18:00 Needleman Wunsch exercise, MSA algorithms Stöver, Ben  

Week 2

Date Time Topic Lecturer Slides
Mon, Feb 9, 2015 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 - 15:30 MP exercise, MP with MEGA Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
15:30 - 18:00 Seminar preparation  
Tue, Feb 10, 2015 10:15 - 12:00 Maximum Likelihood Stöver, Ben Power Point (3 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 15:30 Maximum Likelihood with GARLI and RAxML Stöver, Ben  
15:30 - 18:00 Seminar preparation  
Wed, Feb 11, 2015 10:15 - 12:00 Model- and hypothesis tests with HyPhy Wicke, Susann PDF slides (1 MB)
13:00 - 15:30 Model- and hypothesis tests with HyPhy Wicke, Susann  
15:30 - 18:00 Seminar preparation  
Thu, Feb 12, 2015 10:15 - 12:00 Bayesian statistics, MCMC Stöver, Ben Power Point (3 MB) PDF slides (2 MB) PDF overview (1 MB)
13:00 - 16:00 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 - 18:00 Seminar preparation  
Fri, Feb 13, 2015 10:15 - 12:00 Divergence age estimation Müller, Kai  
13:00 - 15:30 Divergence age estimation Wicke, Susann  
15:30 - 18:00 Seminar preparation  

Week 3

Date Time Topic Lecturer Slides
Mon, Feb 16, 2015 Rosenmontag  
Tue, Feb 17, 2015 Seminar preparation  
16:00 - 17:00 IEB seminar  
Wed, Feb 18, 2015 10:15 - 12:00 Using R for phylogenetics Wicke, Susann  
13:00 - 15:30 Using R for phylogenetics Wicke, Susann  
15:30 - 18:00 Seminar preparation  
Thu, Feb 19, 2015 Seminar preparation  
Fri, Feb 20, 2015 10:15 - 12:00 Student seminars Müller, Kai Wicke, Susann  
13:00 - 15:30 Student seminars Müller, Kai Wicke, Susann  
15:30 - 18:00 Seminar preparation  

Week 4

Date Time Topic Lecturer Slides
Mon, Feb 23, 2015 Time for preparation of the exam  
Tue, Feb 24, 2015 Time for preparation of the exam  
Wed, Feb 25, 2015 10:15 - 11:30 Student seminars Stöver, Ben Wicke, Susann  
Wed, Feb 25, 2015 11:30 - 12:30 Opportunity to ask questions in preparation for the exam Stöver, Ben Wicke, Susann  
Time for preparation of the exam  
Thu, Feb 26, 2015 Time for preparation of the exam  
Fri, Feb 26, 2015 10:15 - 12:00 Exam Wicke, Susann  

Textbooks and resources

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