I want to generate some DNA sequence data  violated reversibility assumtion. Do you know what program can do that? Thanks.

Dear jxn,

HyPhy can do this fairly easily : you would need to define a non-reversible substitution model and then use Simulate to generate some data under that model. Were you looking to simulate nucleotide data?

Cheers,
Sergei

Hi, Sergei

I want to simulate nucleotide data. Would you please show me the  relevant command or/and example that I can start from? thanks a lot.

JXN

Dear jxn,

How do you wish to specify the input? A tree with branch lengths and a number of sites as well as substitution rates?

Cheers,
Sergei

Hi, Sergei

I want to input a tree with branch length, number of the sites. As well as the base frequence and the asymmetric relative rate matrix for the non-reversible substitution model. Thanks a lot.

jxn

Dear jxn,

Do you want the frequencies to be at equilibrium or not? If not, then branch lengths (in the traditional sense) are harder to compute...

Cheers,
Sergei

Hi, Sergei  

I want the frequencies at equilibrium, so the stationary assumption holds.

why do I need to compute the branch lengths? I only need the data simulated under a model which the reversibility doesn't hold.

Thanks.
jxn

Dear jxn,

OK; stationarity makes things easier, but you have 3 constraints on 12 rate parameters to make sure that f_A, f_C, f_G and f_T you stipulate are the stationary distribution.

One needs to convert branch lengths (expected subs/site) into model parameters to simulate the data. I'll put something together tonight.

Cheers,
Sergei

Dear jxn,

Here's an example file for NR simulation (look at the top of the source for user configurable parameters). You need a recent version of HyPhy to run this (for proper output formatting...)

Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Cheers,
Sergei