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v1.2

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@zhangrengang zhangrengang released this 15 Mar 13:07
· 46 commits to master since this release
  1. change some defualt parameters to speedup: -ltr_detectors: ltr_finder,ltr_harvest -> ltr_harvest, -tree_method: iqtree -> FastTree, -tree_options: " -mset JTT" -> "".
  2. 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.
  3. group continuous bins of both potential exchanges and non-exchanges.