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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Simulations of Partitioned Models http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1138099193 Message started by jamescotton on Jan 24^th, 2006 at 2:39am

Title: Simulations of Partitioned Models
Post by jamescotton on Jan 24^th, 2006 at 2:39am

Hi Sergei,

If I simulate data using a model that's partitioned, will the simulated data also have the same partitioning? i.e. if site 3 comes from model 1 in the input data, will site 3 in the simulation also come from this model?

Thanks,
James

PS - I'm also submitting a bug to bugzilla - Hyphy has been crashing on one of my scripts. Of course, the bug could be in my batchfile.

Title: Re: Simulations of Partitioned Models
Post by Sergei on Jan 24^th, 2006 at 7:50am

Dear James,

If you simulate partitioned data through SimulateDataSet (i.e. based on a likelihood function fit), then the sites in the simulated dataset will be arranged contiguously by partition. For example, if in the original data, two hypothetical partitions were 1-20 + 101-150 and the second partition 21-100, then in the simulated data set, sites 1-70 would come from partition one and 71-150 - from partition two.

Cheers,
Sergei