- fixed a bug were the scaling of observed phi values was used inconsitently, causing problems with estimates of Aphi and Sepsilon
- Added SCUO calculation and improved getCSPEstimates to include reference codons
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fixed problem with getCSPEstimates where log scaling was falsely enabled
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fixed problem where the grouplist was not stored by writeParameterObject
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Added functions to calculate the Codon Adaptation Index, Effective Number of Codons and selection coefficients.
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Allow to set initial phi values based on observed phi values stored in genome object.