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.

Deadline for completed applications is on March 15th.



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.


- 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

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
- 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
Take a look at our website ---


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