A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model.

• publication
• 07-01-2006

Catanzaro D, Pesenti R, Milinkovitch MC. Bioinformatics 2006 Mar;22(6):708-15. btk001. 10.1093/bioinformatics/btk001.

The general-time-reversible (GTR) model is one of the most popular models of nucleotide substitution because it constitutes a good trade-off between mathematical tractability and biological reality. However, when it is applied for inferring evolutionary distances and/or instantaneous rate matrices, the GTR model seems more prone to inapplicability than more restrictive time-reversible models. Although it has been previously noted that the causes for intractability are caused by the impossibility of computing the logarithm of a matrix characterised by negative eigenvalues, the issue has not been investigated further.

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