Phylogenomics Course - Agenda.

James McInerney james.o.mcinerney at MAY.IE
Mon Mar 8 09:21:11 EST 2004


Hi folks,

Here is the agenda for the upcoming phylogenomics practical course.

http://bioinf.may.ie/phylogenomics/

Deadline for completed applications is on March 15th.

James



+++++FACULTY++++++


Dr. James McInerney, Maynooth, Ireland.
Dr. Chris Creevey, Maynooth, Ireland.
Prof. T. Martin Embley, Univ. Newcastle, UK.
Dr. Mark Wilkinson, The Natural History Museum, London.
Thomas Keane, Maynooth, Ireland.


+++++TOPICS+++++++

Phylogenies
- Maximum Parsimony.
- Distance Matrix.
- Maximum Likelihood.
- Bayesian methods.

Setting up a phylogenomic infrastructure
- Introduction to UNIX and shell scripting.
- Installation of Fedora (linux).
- Installation of ACNUC  databases.
- Installation of command-line BLAST and FastA software.
- Installation  of PHYLIP, PUZZLE, Mr. Bayes, ClustalW.
- How to turn your desktop or laptop  computer into a phylogenomics
  powerhouse.


Supertrees and Supermatrices
- Introduction to Phylogenetic Supertrees.
- The theory of putting phylogenetic trees with overlapping leaf-sets
  together into a single supertree.
- Phylogenetic supertrees and phylogenetic supermatrices.
- A comparison of the two most commonly-used methods of using large
  datasets, with emphasis on the strengths and weaknesses of each approach.

Distributed computing
- Introduction to distributed systems.
- From MOSIX to MPI.
- How to make an inexpensive supercomputer.
- Using the NUI Maynooth beowulf cluster.
- Parallel approaches to maximum likelihood tree reconstruction
  (DCPml).
- Installation and use of parallel ML software.
- How to get all the computers in your institution to work together as a
  single ML supercomputer.

Discussion and Student data


-- 
Dr. James O. McInerney,
Bioinformatics Laboratory,
Department of Biology, National University of Ireland,
Maynooth, Co. Kildare, Ireland.
P: +353 1 708 3860
F: +353 1 708 3845
E: james.o.mcinerney at may.ie
--
Take a look at our website --- http://bioinf.may.ie/
--


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