Hi,
I have a problem concerning the Ortholog export function of Mauve.
When aligning 5 bacterial genomes (2.2 Mb) certain CDS are recognized as
orthologues while when aligning these 5 genomes and additional 13 genomes
(all from the same bacterial species) the CDS are not recognized as
orthologues in the 5 initial genomes anymore.
Decreasing Coverage and Identity specification didn't help.
Also when I look at the alignments the corresponding regions (Annotation) in
the 5 initial genomes are less perfectly aligned in the alignment of 18
genomes compared to that of the 5 genomes.
I do not understand in detail how mauve works internally, so I have problems
to come up with an Idea how to fix this.
Has anybody experienced this, too? Is there a solution? Have I missed
something?
I'd be very grateful for any help!
Best, Johanna
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