Molecular Systematics BIOL 793T – Syllabus

Guidelines for your final paper - Author instructions for Molecular Phylogenetics and Evolution

Lectures and other daily resources: (subject to change, please return for updates)

Jan 17 - Lecture, Tree thinking quiz 1

Jan 22- Lecture, Baum et al. 2005, Tree thinking quiz 2,

Jan 24 - Lecture, Graur and Li - Chapter 4, Obtain Cluster account for later use

Jan 29 - Lecture, Cherry et al. 1978, Poe 1996, Gatesy et al. 2003

Jan 31- Lecture

Feb 5- Lecture, Mallet 2007, Baker and Bradley 2006, Bickford et al. 2007

Feb 7- Lecture, Submit project topic for approval

Feb 12- Lecture, Giribet and Wheeler 1999, Kumar and Filipski 2007

Feb 14 - Lecture, Lebrun et al. 2006

Feb 19 - Lecture, Hollich et al. 2005

Feb 21- PHYLIP, PAUP quickstart tutorial, PAUP commands, MEGA, de Queiroz and Gatesy 2007

Feb 26 - Lecture, Lipscomb 1998, Graybeal 1998, Hang et al. 2007, Midterm distributed

Feb 28 - Lecture, Slack et al. 2007, Piskurek and Okada 2007, Midterm due

March 4 - Class cancelled

March 6 - Heraty et al. 2007

March 11 - Lecture

March 13 - Submit paper for discussion, Slack 2007

March 18 - Lecture, Hall and Salipante 2007, Bucknam et al. 2006

March 20 - Lecture, Huelsenbeck et al. 2001, Jow et al. 2002, Hall 2005

April 1 - Lecture, Magri et al. 2007

April 3 - Lecture, Hedges and Kumar 2003, Graur and Martin 2004, Pereira and Baker 2006

April 8 - Presentation of papers chosen by students

April 10 - Presentation of papers chosen by students

April 15 - Guest lecture by Jeff Wells

April 17 - Presentation of papers chosen by students

April 22 - Student project presentations

April 24 - Student project presentations

April 29 - Student project presentations

May 1 - Term papers due

Class Discussion Schedule: (subject to change, please return for updates)

Jan 29 - Jeremy Smith, ppt; David Ray, ppt

Feb 7- Christine Picard, ppt

Feb 12- Lizmery Suarez, ppt; Michelle Thompson, ppt

Feb 14 - Michelle Thompson, ppt

Feb 19 - Adam Hnatkovich, ppt

Feb 21- Baneshwar Singh, ppt

Feb 26 - Tiffany Smith, ppt; Heidi Pagan, ppt

March 4 - Heidi Pagan, ppt

March 6- Christine Picard, ppt; ???, ppt

March 11 - no presentations

March 13 - Lizmery Suarez, Slack 2007, ppt

March 18 - Tiffany Smith, Hall and Salipante 2007, ppt; Baneshwar Singh, Bucknam et al. 2006, ppt

March 20- Lizmery Suarez, Jow et al. 2002, ppt; Adam Hnatkovich, Hall 2005, ppt

April 1 - Rodney Dever, Magri et al. 2007, ppt

April 3- Jeremy Smith, Graur and Martin 2004, ppt; Rodney Dever, Pereira and Baker 2006, ppt

April 8- Name, ppt;

April 10- Name, ppt;

April 17 - Name, ppt;

April 22- Name, ppt;

April 24 - Name, ppt;

April 29 - Name, ppt;

May 1 - Name, ppt;

Data for exercises:

Software resources:

Phylogeny estimation:

MEGA - http://www.megasoftware.net/

PAUP (Phylogenetic Analysis Using Parsimony) - PAUP quickstart tutorial, PAUP commands

PHYLIP (PHYLogeny Inference Package) - http://evolution.genetics.washington.edu/phylip.html

MrBayes - http://mrbayes.csit.fsu.edu/

BAMBE (Bayesian Analysis in Molecular Biology and Evolution) - http://www.mathcs.duq.edu/larget/bambe.html

PAML (Phylogenetic Analysis by Maximum Likelihood) - http://abacus.gene.ucl.ac.uk/software/paml.html

Mac5 - http://www.agapow.net/software/mac5

Bali-Phy - http://www.biomath.ucla.edu/msuchard/bali-phy/

PhyML - http://atgc.lirmm.fr/phyml/

Sequence alignment:

ClustalX - http://bips.u-strasbg.fr/fr/Documentation/ClustalX/

MUSCLE - http://www.drive5.com/muscle/

Tree manipulation:

Treeview - http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

Treesnatcher - http://www.cibiv.at/software/treesnatcher/

FigTree - http://tree.bio.ed.ac.uk/software/figtree/

Evolutionary model estimation:
ModelTest - http://darwin.uvigo.es/software/modeltest.html
MrModelTest - http://darwin.uvigo.es/software/modeltest.html

ProtTest - http://darwin.uvigo.es/software/prottest.html

Misc.:

BioEdit - http://www.mbio.ncsu.edu/BioEdit/bioedit.html

MacClade - http://macclade.org/macclade.html
Geneious - http://www.geneious.com/

FaBox (an online fasta sequence toolbox) - http://www.birc.au.dk/fabox/

ReadSeq (biosequence conversion tool) - http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi

A local version of the Sequence Manipulation Suite: http://www.as.wvu.edu/~dray/sms2/

If you can't find what you need here, try http://evolution.genetics.washington.edu/phylip/software.html