Skip to main content

Table 1 Rate parameters

From: TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column

\(R_{\text {Symmetric}} = \begin{pmatrix} * &{} \alpha &{} \beta &{} \gamma \\ \eta &{} * &{} \delta &{} \epsilon \\ \epsilon &{} \delta &{} * &{} \eta \\ \gamma &{} \beta &{} \alpha &{} * \end{pmatrix}, R_{\text {GTR}}= \begin{pmatrix} * &{} \pi _A \alpha &{} \pi _A \beta &{} \pi _A \gamma \\ \pi _C \alpha &{} * &{} \pi _C \delta &{} \pi _C \epsilon \\ \pi _G \beta &{} \pi _G \delta &{} * &{} \pi _G \eta \\ \pi _T \gamma &{} \pi _T \epsilon &{} \pi _T \eta &{} * \end{pmatrix}\)

  1. \(R_{\text {Symmetric}}\) and \(R_{\text {GTR}}\) represent the rate parameters of strand symmetric and general time reversible (GTR) models, respectively. Matrix indices are ordered such that \(i,j\in \{1,2,3,4\}=\{A,C,G,T\}\). \(\pi _{*}\) is the equilibrium distribution of the GTR model. Diagonal elements are determined by the Markov condition \(\sum _{i}R_{ij}=0\)
Back to article page

Algorithms for Molecular Biology

ISSN: 1748-7188