sequence evolution simulator

Question

[Abdullah]

Hi,

I have a set of sequences and a tree topology for these sequences.

Is there an available tool that can make random mutations to the sequences given a specific position on the tree?

assuming I have this tree : (A,(B,(C,D)1)2)3;

A,B,C and D are species inside the tree.

I want to lets say select internal node 3 and make one random mutation to all species within this node.

Then take node 2 and make one other random mutation to all species there... and so on for all internal nodes in the tree where the choice if a mutation exists or no on this edge is also chosen randomly.

Is there any available tools? Otherwise I would implement one on my own?

Answer 1

[David W]

You are pretty much describing seq-gen, which allows you to use different models of seqeunce evolution and actually places mutations on branches rather in nodes (or, at last, takes branch lengths into account when simulating mutations).