We wish to introduce Clann, Software for investigating phylogenomic
information using supertrees.
The word "Clann" is the Irish word for "family".
This version of Clann (2.0.1) 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)
Clann is freely available to the scientific community at:
http://bioinf.may.ie/software/clann/
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