What is the best tool to identify and provide a good pictorial representation of homologous DNA sequences between species?

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Gregory Dressler

Use the UCSB genome browser (genome.ucsb.edu) and select the full conservation icon under the comparative genomics menu and the browser will show you tracks of homology among divergent species.

Albino Bacolla

You may try Clustal omega at https://www.ebi.ac.uk/Tools/msa/clustalo/

and see if by turning on the colors it will give you a good representation of your data.