[Primeusers] Cannot run program

[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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