| Calling Sequence
| CodonMatrix()
CodonMatrix(Sim, Desc, CodonPam)
CodonMatrix(Sim, Desc, CodonPam, AAPAM)
CodonMatrix(Sim, Desc, CodonPam, AAPAM, FixedDel, IncDel)
|
| Parameters
| | Name | Type | Description |
|
| Sim
| matrix(numeric,64) | 64 x 64 codon similarity matrix |
| Desc
| string | a description |
| CodonPam
| numeric | CodonPam number of the matrix |
| AAPam
| numeric | the equivalent PAM distance |
| FixedDel
| numeric | the constant part of the deletion costs |
| IncDel
| numeric | the length-dependent part of the deletion costs |
| PamDistance
| numeric | synonym of CodonPam |
| PamNumber
| numeric | synonym of CodonPam |
| MaxSim
| numeric | the highest similarity score in the matrix |
| MinSim
| numeric | the lowest similarity score in the matrix |
| MaxOffDiag
| numeric | the highest similarity score that is not in the diagonal |
| Type
| string | synonym of Desc |
| Description
| string | synonym of Desc |
|
| Methods
| lprint, print, Rand, select, string |
| Synopsis
| A CodonMatrix contains everything that is needed to score
codon alignments.
This is basically the 64x64 scoring matrix plus the deletion cost function.
These costs are based on the PAM distance equivalent and are
calculated automatically if they are not given as an argument.
A CodonMatrix is now only used for teh SynPAM matrices |
| See also
| CodonPamToPam, CreateSynMatrices, PamToCodonPam |