Pathological rate matrices: from primates to pathogens
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Schranz, Harold; Easteal, Simon; Huttley, Gavin Austin; Yap, Von Bing; Knight, Rob
BACKGROUND: Continuous-time Markov models allow flexible, parametrically succinct descriptions of sequence divergence. Non-reversible forms of these models are more biologically realistic but are challenging to develop. The instantaneous rate matrices defined for these models are typically transformed into substitution probability matrices using a matrix exponentiation algorithm that employs eigendecomposition, but this algorithm has characteristic vulnerabilities that lead to significant...[Show more]
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