creating multiple sequence alignments for plants

[colindaven]

Hi,

I work on plants, which seem to be lacking with the precomputed MSAs available.

What software would you recommend for creating genome scale MSAs of plants ? I can think of pangenome software like PGGB and minigraph-cactus, and converting from odgi to MSA formats, but I don't know of other reliable non-graph based alternatives.

Thanks