iPE::Model::BNTree(3)

NAME
iPE::Model::BNTree - A Bayesian Network Tree model for N-SCAN.

DESCRIPTION
This is not a traditional model in the sense of owning parameters themselves, it simply contains a tree topology and a model type. It will accept counts in the form of a hash, and return the text needed by N-SCAN for a parameter file via the optimize function.

Example of phylogenetic tree:

        "[[galGal2:4,[mm5:2,rn3:3]],none]"

The tree is re-rooted at the target which, in this case, is human. The target is not listed explicitly in the tree; it is listed separately. The informants are chicken (galGal2), mouse (mm5), and rat (rn3). The numbers following the species names and colon refer to the order in which the each species occurs in the alignment file. For example, mouse - second, rat - third, and chicken - fourth.

Valid N-SCAN models are:

TT - Transition/transversion model.
R  - Reversible matrix.  Probability of a transition from node a to node b is equal to transition from node b to node a.
G - Generalized.  All transitions, forward and reverse, are estimated.
    Generally speaking, a first order reversible model (R1) is used. All models must have an accompanying order number, (TT0, TT1, .. , G0, etc.) in the specification.

METHODS

new (topology, model-type)
    Pass a topology and model type to retrieve a BNTree object. See above for descriptions of these items.

SEE ALSO
iPE iPE::Model::Emission

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu).