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I would like to get the percentage of similitude of two genomic sequences, the supercontigs are obtained from:

http://www.broadinstitute.org/annotation/genome/neisseria_gonorrhoeae/MultiDownloads.html

(the above is just an example), the problem that I have is when I want to use the tool known as MultiPipMaker http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker/?

this tool allows to upload two DNA sequences in FASTA format and returns the similitude between the secuences. The issue that I have is that when the sequences are too big (> 4 Mb) the results appears with an error, saying that the blastz CPU time limit exceeded. The question that I have is how I can get the percentage of similitude with this type of tool? It seems that it cannot hold large sequences, even though in its papers it says the opposite.

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what is similitude ? Please elaborate about what you seek from this procedure. Moreover, if this is in particular about a specific bioinformatics tool then i would suggest that you ask this question in biostar. –  WYSIWYG Nov 4 '13 at 16:47
    
I mean to know how similar or percentage of equality between a couple of genomes. I have tried biostar before, but it takes ages to get an answer –  Layla Nov 5 '13 at 13:29
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