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question of how to perform alignment for .gff sequences

Hi there, im trying to do alignment on some mamalian genome annotations, at first i tried to do so on LASTZ, but it does not accept the .gff file as target or query. now i have 2 questions 1: is it wrong to try to perform alignment between two annotated genome against each other? 2: plz introduce me some other tool , preferably on the galaxy server, to do long genome alignment for .gff files. Thank you all.

alignment genome
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written by asghari.be • asghari.be

Does the gff contain sequences?

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written by h.mon h.mon

The gff contains the annotation sequence of genome

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written by asghari.be • asghari.be

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