General information

  • Start of the course: Mon, Feb 6, 2012, 10 s.t. (room 0431 100 10)
  • Room: Lecture: 0431 100 10 (Kursraum), Practical: 0431 100 14 (CIP-Pool), both in the basement of the IEB, Hüfferstraße 1
  • Course folder on NWZNET: N:\Group\Biologie\r0muelle\Teaching\WS 2011 2012\130313 Molecular Phylogenetics (Via VPN you can also access these files from your home either directly (see here for details) or with a remote desktop connection via nwzhome.nwznet.uni-muenster.de.)
  • Exam: The exam will be on Fri, Mar 2, 2012, 10:00 a.m. at the IEB lecture hall (room 0431 100 32, basement of the IEB).
    • Download example questions
    • There is an opportunity to ask questions releted to the lecture in preparation for the exam on Thu, Mar 1, 2012, 15:00 in room 0431 100 10.

Time table

Lecture

Date Topic Lecturer Slides
Mon, Feb 6, 2012 Introduction to phylogenetics Müller, Kai Power Point (10 MB) PDF slides (5 MB) PDF overview (3 MB)
Tue, Feb 7, 2012 Maximum Parsimony, tree searches, bootstrapping, Bremer support Müller, Kai Power Point (5 MB) PDF slides (3 MB) PDF overview (2 MB)
Wed, Feb 8, 2012 Distances Müller, Kai Power Point (4 MB) PDF slides (3 MB) PDF overview (1 MB)
Thu, Feb 9, 2012 Maximum Likelihood Müller, Kai Power Point (2 MB) PDF slides (2 MB) PDF overview (1 MB)
Fri, Feb 10, 2012 More realistic models Müller, Kai Power Point (2 MB) PDF slides (1 MB) PDF overview (1 MB)
Mon, Feb 13, 2012 Bayesian statistics Müller, Kai Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
Tue, Feb 14, 2012 Divergence age estimation Müller, Kai Power Point (1 MB) PDF slides (2 MB) PDF overview (1 MB)
Wed, Feb 15, 2012 Model- and hypothesis tests, topology tests etc. Müller, Kai Power Point (2 MB) PDF slides (2 MB) PDF overview (1 MB)
Thu, Feb 16, 2012 NGS data -> Assembly of plastid genomes -> HyPhy Wicke, Susann Power Point (14 MB) PDF slides (6 MB) PDF overview (3 MB)
Fri, Feb 17, 2012 Hypothesis testing: practical examples

This lecture will take place in room 0431 120 208 (conference room on the second floor).
Wicke, Susann  
Tue, Feb 21, 2012 Multple sequence alignment Stöver, Ben Power Point (1 MB) PDF slides (1 MB) PDF overview (1 MB)
Wed, Feb 22, 2012 Orthology prediction Terrapon, Nicolas PDF slides (2 MB)
Thu, Feb 23, 2012 Functional annotation Terrapon, Nicolas PDF slides (5 MB)
Fri, Feb 23, 2012 Domain rearrangements Bornberg-Bauer, Erich PDF slides (6 MB)
Mon, Feb 26, 2012 Next generation sequencing Franssen, Susanne PDF slides (2 MB)
Tue, Feb 27, 2012 Assembly Grath, Sonja PDF slides (1 MB) Additional information (1 MB)

Download additional information to the lecture (12 MB).

Practical

Date Topic Lecturer
Mon, Feb 6, 2012 Kommandozeile, Phylogenetische Dateiformate, Baum- und Alignmenteditoren Stöver, Ben
Tue, Feb 7, 2012 Parsimony, Bootstrap, Jackknife: PAUP* Stöver, Ben
Web, Feb 8, 2012 Distanzen: MEGA, PAUP* Stöver, Ben
Fri, Feb 10, 2012 1. Paper-Besprechung Müller, Kai
Mon, Feb 13, 2012 Maximum Likelihood: GARLI, Raxml Stöver, Ben
Thu, Feb 14, 2012 Bayesianische Statistik: MrBayes, Divergence age estimation: BEAST Stöver, Ben
Wed, Feb 15, 2012 Ancestral state reconstruction: Mesquite, BayesTraits; Topological tests: Consel; Model tests: ModelTest Stöver, Ben
Thu, Feb 16, 2012 2. Paperbesprechung (Download) Müller, Kai
Fri, Feb 17, 2012 Hypothesis tests: HyPhy Stöver, Ben
Tue, Feb 21, 2012 Automated multiple sequece alignment Stöver, Ben
Wed, Feb 22, 2012 Orthology prediction Terrapon, Nicolas
Thu, Feb 23, 2012 Functional annotation Terrapon, Nicolas
Fri, Feb 23, 2012 Domain rearrangements Moore, Andrew
Mon, Feb 26, 2012 Next generation sequencing Franssen, Susanne
Tue, Feb 27, 2012 Assembly Grath, Sonja

Software

The following phylogenetic software will be used in the course. You can either download the software from the linked developer sites or download an archive containing all software (173 MB, 8.02.2012), except PAUP* due to licencing.

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
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.)
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 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.
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.

Pages that list additional phylogenetic software