| Calling Sequence
| CodonMutate(seq1,cpam)
CodonMutate(seq1,cpam,DelType,lnM1)
|
| Parameters
| | Name | Type | Description |
|
| seq1
| string | codon sequence |
| cpam
| positive | CodonPAM distance to mutate |
| DelType
| ExpGaps | (optional) gap type |
| lnM1
| matrix(numeric) | (optional) log. of a 1-PAM matrix |
|
| Return Type
| string |
| Synopsis
| Mutates a sequence of codons over a certain CodonPAM distance.
Stop codons always mutate to stop codons while sense codon always mutate to sense
codons. When a gap type is given, the function returns not only the mutated string,
but also the two aligned sequences, where the exact position of the gaps can be
seen. lnM1 is by default assumed to be CodonLogPAM1 which must be created with
CreateDayMatrices() first. |
| Examples
| > CodonMutate(CCCATCAACACTGAC,50);
CCTATCGCCACCGAC
|
| See also
| CreateCodonMatrices, CreateRandSeq, Mutate |