What software can I use to compare two annotated genomes downloaded from NCBI database?

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Mohamad Al Kadi

I don't know what you are exactly looking for. If you want to browse two annotations and compare them you can use IGV. First download the genome (create a genome file from the fasta file and one of the annotations). Then you can simply open the other annotation. You will have two tracks for each annotation. I hope this is what you are looking for.

Yu-Chen Liu

Article Comparative Genomic Analysis Using the UCSC Genome Browser

I remembered UCSC has tools for different purposes for that?