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Any suggestion for tools to find percentage similarity between two genomes? I have proteome file for these genomes.
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Mummer might be what you're looking for, which first requires aligning the two genomes.
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or Artemis Comparison Tool. http://www.sanger.ac.uk/resources/software/act/
ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotationComment
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Thanks Peter and yl!Comment
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