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Hi could someone explain to me what exactly the '-fat' option of mummerplot does? I am a bit confused and could not find a satisfying answer…
It is similar to the -layout option, but uses a different heuristic for ordering and orienting the aligned sequences. -layout tried to line up the beginning and ends of sequences, while -fat tries to line up the "heaviest" alignment for each sequence. For simple cases, the two should produce similar output. Try it on a complex layout, with many fragmented mappings, and you'll start to see the difference.