[Primeusers] Cannot run program

[arve]

Hi Anita,
The error you get should only occur if the file is not found. Have you double checked the name of the file and its location?

Yes, there are several parameters that you need to specify at this point, for the simple reason that we have not implemented their inference yet. 

We do not support partitioning of data at this point.

	Best regards,
	Lars

Jan 26, 2010 kl. 3:10 PM skrev A.Malhotra:

> I am trying to run an analysis using PrimeGSR but get an error message 
> saying "could not open sequence file". However, this file is in fasta 
> format and I can open it in other programs so there seems to be nothing 
> wrong with it.
> 
> primeGSR -o PLA2.out -i 10000000 -t 2000 -w 100 -Su DNA Pi=0.2560 0.2748
> 0.2332 0.236 R=1.5842 4.2435 1.0570 1.5330 4.6701 1.0 -Sn 4 -Sa 0.7564
> -Ed Gamma -Hi vipers.tre nc_nr.fa gs.txt
> 
> I would also appreciate some guidance about setting the model. Normally
> when running a Bayesian phylgenetic analysis (eg in MrBayes) I would not
> set all the parameter values at the beginning but let the Markov chain
> integrate over the uncertainty in these values. However it seems that
> primeGSR requires you to input them. Is this correct and if so, why? 
> Finally, I wonder is it is possible to analyse partitioned data in 
> primeGSR (eg in MrBayes I can include gaps in the form of a simple-coded 
> matrix as a separate partition)?
> Thanks
> Anita
> 
> -- 
> *******************************************************************
> Dr Anita Malhotra         	e-mail: a.malhotra at bangor.ac.uk
> School of Biological Sciences	Tel(direct line): + 44 1248 383735
> College of Natural Sciences	Fax: + 44 1248 371644
> Bangor University		
> 3rd Floor ECW
> Deiniol Road, Bangor		
> Gwynedd LL57 2UW
> United Kingdom
> *******************************************************************
> 
> 
> -- 
> *******************************************************************
> Dr Anita Malhotra         	e-mail: a.malhotra at bangor.ac.uk
> School of Biological Sciences	Tel(direct line): + 44 1248 383735
> College of Natural Sciences	Fax: + 44 1248 371644
> Bangor University		
> 3rd Floor ECW
> Deiniol Road, Bangor		
> Gwynedd LL57 2UW
> United Kingdom
> *******************************************************************
> 
> -- 
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