Unexpected output

[medvedevgroup]

Unexpected output

[iminkin]

Hi,

I am glad that you found SibeliaZ helpful. This is a bit tricky question. Representation of whole-genome alignment is inherently ambiguous. For example, a single alignment block can be chopped into multiple consecutive blocks and still represent an equivalent alignment. Also, the newer version could generate more blocks due to improvements in sensitivity, which would also result in fragmenting the blocks, which I suspect is the case. Does the coverage change of the block change significantly between the runs of different versions?

Regarding to -a option, it depends on how many genomes are there in the dataset, as well as their repeat content. What kind of genomes (and how many) are you trying to align?