I have performed numerous simulations of nucleotide sequence evolutions down phylogenetic trees, but I would now like to try something a little different. I am having difficulty locating software to perform this task and would like to ask for your advice.
I would like to take a haploid genome (e.g. bacterial or mitochondrial) of a given length and nucleotide composition, and then forward simulate the evolution of this genome with the following inputs:
- Markov model of nucelotide substitution including a distribution of relative rate of substitution across sites
- A population growth parameter
- Generation time
As the title suggests, I'd like this to be a tree-independent process (part of what I am investigating are the characteristics of the phylogenetic tree that can be reconstructed for the simulated final population).
Further, I'd like to be able to manually input the characteristics of my substitution model and rate distribution - I have reason to believe that none of the usual suspects (i.e. GTR, TN etc. and the typical gamma distribution of rate categories) describe my real dataset particularly well.
Does anyone know of any software capable of performing something like this?
Thank you for your time.