How to align the genomes at conting or scaffold level？

[naturalstay]

Hello, Dr Song, Thank you for developing such a powerful tool. When I use it, I find that the genomes seem to must be at the level of chromosome assembly. But some of my genomes are at the level of contig or scaffold, I am not sure whether the genome at the contig and scaffold levels can be used. If not, do you have any great suggestions？ Thank you very much and look forward to your reply.

[baoxingsong]

Hi, it is hard to perform collinear analysis with short contigs or scaffolds. The collinearity algorithm implemented in AnchorWave requires 3 collinear genes to identify a collinear block.