Can AnchorWave be used for calculating identities of pairwise alignments in whole genome comparisons?

[cjchen5]

Dear AnchorWave team,

I am currently working on a project that involves calculating identities of 1M window size pairwise alignments in whole genome comparisons. I understand that AnchorWave is designed for sensitive alignment of genomes with high sequence diversity and extensive structural polymorphism. I am wondering if AnchorWave could be used to assist in my project. Specifically, can it help me calculate identities of 1M window size pairwise alignments in whole genome comparisons?

Thank you for your time and assistance!