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change some defualt parameters to speedup: -ltr_detectors: ltr_finder,ltr_harvest -> ltr_harvest, -tree_method: iqtree -> FastTree, -tree_options: " -mset JTT" -> "".
new options: -sg_assigned to provide subgenome priors (will not re-assign subgenome), -exclude_exchanges to exclude exchagnes for LTR insertion age estimation, -chr_ordered and -alt_cfgs to manage the order and homoeologous relationships of chromosomes in the circos plot.
group continuous bins of both potential exchanges and non-exchanges.