| Calling Sequence
| Mutate(seq,PAM,DelType)
|
| Parameters
| | Name | Type | Description |
|
| seq
| string | original amino acid sequence |
| PAM
| numeric | desired PAM distance to mutate |
| DelType
| {ExpGaps,ZipfGaps} | optional, model for making gaps |
|
| Return Type
| string |
| Synopsis
| This function simulates evolution by performing
random mutations in an amino acid sequence. These random mutations
respond to the PAM distance given. The mutations will respond to
a mutation matrix at that distance. If the third argument is given,
the gaps will be inserted, either with an exponential or zipfian
distribution. If no third parameter is given, no gaps will be
inserted.
Mutate will use the mutation matrices available in logPAM1, which
are normally set by CreateDayMatrices().
If these matrices are created for DNA (only A,C,G and T), then
the function Mutate will mutate a DNA sequence. |
| Examples
| > Mutate(CreateString(40,A),100);
GAVAATFLSAKPDPGGRGSLPTAASTAESHSTARTAASGG
|
| See also
| CreateDayMatrices, CreateRandPermutation, CreateRandSeq, Shuffle |