Support question: End-to-end chromosome alignments with progressive cactus

[JohnLloyd-Bayer]

Can progressive cactus be coerced to align chromosomes end-to-end for multiple individuals of the same species? I have run progressive cactus, and the output alignments include multiple regions of a chromosome in the same alignment, it does not have the chromosomes aligned end-to-end. By comparison, cactus (not "progressive") provides this type of end-to-end chromosome alignment, but I am interested in the compute efficiency provided by progressive cactus to provide a similar output. I am working in corn (Zea mays), which has a large-ish genome (2.3Gb) and is highly repetitive with low sequence conservation in intergenic space, so scaling the cactus pipeline (not "progressive") to hundreds of corn individuals is a computational challenge.