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Optimal Dirichlet models
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This directory gives optimal 1-simplex (Dir(alpha)_m) and 2-simplex Dirichlet model (Dir(alpha)_i) parameters for each of the 9 existing matrices and the 6 inferred matrices across each of the 6 benchmarks.

Dir(alpha)_m corresponds to Pr(m|m) free parameter.
(Denote Dir(alpha)_m parameter vector as {a1,a2})
Dir(alpha)_i corresponds to Pr(i|i) and Pr(m|i) free parameters.
(Denote Dir(alpha)_i parameter vector as {a1,a2,a3})

Optimal Dirichlet models for BLOSUM and PFASUM matrices are present only for SCOP2 benchmark. 

Each file is in the following format: 

<Evolutionary distance t> <Dir(alpha)_m_a1> <Dir(alpha)_m_a2> <Dir(alpha)_i_a1> <Dir(alpha)_i_a2> <Dir(alpha)_i_a3> 

NOTE: Some t values are missing in terms of different matrices and benchmarks due to benchmark compositional differences. 