This protocol is based on the procedure that we used to analyze the homologous chromosomal region of the ladybird beetle color pattern locus. We mainly use Easyfig software and provide an additional custom Perl script and a test dataset for fine visualization of chromosomal similarities.
You can read a Japanese commentary on this protocol in Jisedai Sequencer DRY Kaiseki Kyohon 2nd Ed (次世代シーケンサーDRY解析教本 改訂第２版), Gakken Medical Shueisha, Tokyo, 2019, pp369-370.