Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states.
A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG.
A reversible amino acid substitution model with rates and frequencies stored in file
matrixDir, rateFile, freqFile, encoding, rates, eigenSystem, frequencies
| type: java.io.File |
| director containing files with empirical rate matrix and empirical frequencies. |
| Optional input |
| type: java.lang.String |
| name of comma separated file containing empirical rate matrix -- can contain new lines, but not comments. |
| Optional input. Default: rates.csv |
| type: java.lang.String |
| name of comma separated file containing empirical frequencies |
| Optional input. Default: freqs.csv |
| type: java.lang.String |
| order im which the amino acids appear in file |
| Optional input. Default: ARNDCQEGHILKMFPSTWYV |
| type: beast.base.core.Function |
| Rate parameter which defines the transition rate matrix. Only the off-diagonal entries need to be specified (diagonal makes row sum to zero in a rate matrix). Entry i specifies the rate from floor(i/(n-1)) to i%(n-1)+delta where n is the number of states and delta=1 if floor(i/(n-1)) <= i%(n-1) and 0 otherwise. |
| Optional input |
| type: java.lang.String |
| Name of the class used for creating an EigenSystem |
| Optional input. Default: beast.base.evolution.substitutionmodel.DefaultEigenSystem |
| type: beast.base.evolution.substitutionmodel.Frequencies |
| substitution model equilibrium state frequencies |
| Optional input |