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Is it possible to use an available known ancestral genome to paint chromosomal rearrangement?

nam-hoang opened this issue · comments

commented

Thank you very much for this wonderful tool.

I wonder if we could use a known ancestral genome (instead of construct it) to analyze the genome rearrangement using this IAGS pipeline? For example, in my case, I am studying the Brassica genomes (including the 3 species that were included in Figure 3A of your paper (B. rapa, B. oleracea and B. nigra) and their ancestral genome tPCK. So, how one could just assign this tPCK genome as a common ancestral genome, and then analyze the rearrangement of the 22 genomic blocks in the extant genomes?

Thank you very much and I am looking forward to hearing from you.
Best regards,
Nam

commented

Yes, you can. You need to make sure tPCK and three Brassica genome shared all blocks and use the scripts in util. You can find details in user guide(docs).