Pileup problem with long sequences

Julie Knott jknott at MOLBIO.CBS.UMN.EDU
Wed Nov 16 20:32:39 EST 1994


PileUp's maximum sequence length is 5kb.  I don't know if it can be 
changed.  It's a lousy parameter, as I have 10-20kb I'd like to see too.  
Please let me know if you find a better way.  I'll be watching the net -- 
does anyone know a better way?

jknott at molbio.cbs.umn.edu

On 16 Nov 1994 jcalvert at crcvms.unl.edu wrote:

> What's the most likely cause of the "alignment may not
> be optimal" message during a pileup alignment of several
> long sequences? The resulting output is clearly not the 
> best alignment. Is this a memory problem? What parameter
> needs to be increased?
> Thanks in advance for helpful suggestions from anyone.
> Jay Calvert     jcalvert at crcvms.unl.edu

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