Best algorithm for simulating the evolution on a DNA sequence

Question

[mahdiks]

Hi Biostars,

I'm developing a footprint for DNA sequence and then I want to find related seq in another sequence. (https://github.com/MahdiKarimian/DIF)

My question is : What is the best available library that simulates the evolution of a sequence of DNA?

I want to use that sequence to check my DNA footprint matching algorithm,

Answer 1

[Michael]

It is maybe less an algorithm than a substitution model you are looking for. This review may be relevant. Just pick a suitable substitution model. The choice depends on under which selection pressure you assume your sequence is. A codon model can be used for protein coding sequences and a DNA model for non-coding sequences, then mutate each given position or codon based on the substitution probabilities given in the matrix in each generation and run this for a number of generations. Possibly, there is an implementation of such a process but I don't know any right now.