pseudo-rate matrices valid?

Andreas Bernauer andreas.bernauer at
Mon Apr 19 00:35:23 EST 2004


I've just computed rate matrices and figured that some off-diagonal
entries are negative (pseudo rate matrix).  I am wondering if anybody
knows, how accepted those matrices are, say for scientifc publication.
 I've searched the web for input on this, but without success on how
accepted pseudo rate matrices are.

Background:  I estimated Q in P = exp(tQ) for a model of amino acid
replacement, where P is the transition matrix of a Markov model.  For
biologocial interpretation, Q's off-diagonals should be positive,
otherwise one gets negative probabilities for small t.

Thank you very much in advance for any comment.

Andreas Bernauer.

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