| Calling Sequence
| CodonPamToPam(lnM1,CF,CodonPam)
|
| Parameters
| | Name | Type | Description |
|
| lnM1
| matrix(numeric,64) | Logarithm of a 1-PAM codon mutation matrix. |
| CF
| array(numeric,64) | Codon frequencies |
| CodonPam
| numeric | CodonPAM to be converted |
|
| Return Type
| numeric |
| Synopsis
| Converts CodonPAM to PAM.
This conversion depends on the amount of synonymous mutations for a
species or set of species, so the logarithm of the 1-CodonPAM matrix
and the codon frequencies are required as arguments.
The conversion is done by summing up the percentage of synonymous
mutations in the codon matrix.
This sum is the expected percentage of identical amino acids at this
CodonPAM distance, which then can be converted to PAM using the
PerIdentToPam function. |
| Examples
| > CodonPamToPam(CodonLogPAM1,CF,50);
23.3413
|
| See also
| CreateCodonMatrices, PamToCodonPam, PerIdentToPam |