Can the anchorwave results be used for subsequent multi-genome alignment?

[WU-WEIHONG]

Hi,

Anchorwave is an excellent plant genome alignment software and can generate sensitive alignment of genomes with extensive SVs and WGDs.

However, it is a pairwise genome alignment tool. Can I use the anchorwave results to perform multiple genome alignment (WGA)?

if practicable, do you have any suggestions for subsequent WGA? Do you have any plans to add WGA function to anchorwave?

[baoxingsong]

Thanks so much for this great point. We tried to put AnchorWave into the ROAST pipeline and also tried to replace the LASTZ in the Cactus pipeline with AnchorWave. But failed for both, ROAST and Cactus cost too much memory for real genome data.

We are trying to design a new graph model to deal with the plant multiple genome alignment problem, especially cross-species with whole genome duplication differences.

[WU-WEIHONG]

Thank you for your answer and really look forward to the new model！