New release of Clann

Chris Creevey chris.creevey at MAY.IE
Tue Nov 16 16:11:03 EST 2004


Hi,
Just to announce that we have released a new version of Clann at:

	http://bioinf.may.ie/software/clann/

For those that may be unfamiliar with Clann:

Clann is a sofware program for investigating phylogenetic information
through Supertree analyses.

Clann has recently been published in Bioinformatics:
http://bioinformatics.oupjournals.org/cgi/content/abstract/bti020v1


This version of Clann (2.0.3) implements four supertree methods (which
are used as optimality criteria):

Matrix Representation using Parsimony (But Paup* is necessary for the
parsimony part)
Maximum Quartet fit
Maximum Split (component) fit
Most Similar Supertree Method (A novel method related to the average
consensus method with branch lengths set to unity)

For each of these optimality criteria, Clann allows:
	Searches of supertree-space using Exhaustive or Heuristic searches
(NNI & SPR)
	Searches of User-defined trees.
	Investigation into the support for various hypotheses through:
		Bootstrapping (at the source tree level)
		YAPTP tests (a randomisation test similar to the ptp test)

New Features:
	Sampling of supertree space before heuristic searches
	Introduction of Neighbor joining on MRP matrices
	Readline library for ease of use
	Several bugs fixed

Clann is freely available to the scientific community at:
	http://bioinf.may.ie/software/clann/


_______________________________________________________________________

Dr. Christopher J. Creevey
Bioinformatics and Pharmacogenomics Laboratory,
Department of Biology,
National University of Ireland, Maynooth
Co. Kildare
Eire.

e: chris.creevey at may.ie
p: + 353 1 708 6043
f: + 353 1 708 3845
w: http://bioinf.may.ie/

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