Images didn't come through, sorry. Please see attached.
On Wed, Mar 1, 2017 at 12:01 PM, Eleni Mijalis <elenimija...@tamu.edu>
wrote:
> Hey there,
>
> I am having issues with getting different alignment results based on the
> ordering of input files.
>
> I am aligning 7 genomes, and this is these are two examples of alignments
> differing based on order:
> [image: Inline image 1]
>
> [image: Inline image 2]
>
> As you can see, the first example gives 1 LCB spanning the entirety of all
> the genomes, and the second example (same genomes, different order) has
> more LCBs spanning different areas of each genome. These two are just
> samples of what output I get based on input permutation.
>
> I am using default parameters, so should I adjust parameters to get more
> consistent results? Why would ordering matter when determining regions of
> similarity? Thanks for your help.
>
> Eleni
>
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