BEAGLE API call | Arrays initialized and coprocessor action |
---|---|
beagleSetEigenDecomposition beagleUpdateTransitionMatrix beagleGetTransitionMatrix | 4x4 transition probability matrices for each node (initialize arrays tipL and tipR in Pseudocode 1) |
beagleSetTipPartials | Copy an array of partials into an instance buffer (initialize arrays clL and clR in Pseudocode 1) |
beagleSetStateFrequencies | Copy a state frequency array into an instance buffer (initialize array bs in Pseudocode 1) |
beagleSetPatternWeights | Set the vector of pattern weights for an instance (initialize array numSites in Pseudocode 1) |
beagleResetScaleFactor | Reset a cumulative scale buffer |
beagleUpdatePartials | Calculate partials for all internal nodes (compute array clP in Pseudocode 1) |
beagleCalculateRootLogLike | Calculate log-likelihood of root node. (compute arrays lnScaler and scP in Pseudocode 1, calculate lnL in Pseudocode 1) |