release for Zenodo

minor revises.

v1.2

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.

v1.1

Revisions:

1. fix a bug of estimating LTR insertion time, which make the time ~2.3-fold larger than the previous.
2. add FDR (column: p_corrected) for p-values and potential exchanges (column: potential_exchange) of enrichments (output file: *.bin.enrich and *.ltr.enrich).
3. add color slides for heatmap axes (coloring by subgenome).
4. add alternative test method such as kruskal (option -test_method) to identify subgenome-specific kmers.
5. other minor revisions.

final version of the new phy paper

v1.0

fix a bug