- to run globally just execute {your MCScanX executable}_h -options MCScanX
like ./MCScanX_h MCScanX if the executable is in current directory
- to draw the inferred MCScanX blocks (with pygenomeviz) execute "python3 mcdraw.py --mcscanx_file {file} --threshold_chr {len_smalleest chr/scaffold/contig to draw (not to clutter the image}". this will use the anchor alignments to infer a greedy pariwise drawing order and then parse the mcscanx blocks and draw them according to the order.
- produce a phylogeny based on anchor alignemtns involved in collinearity chains with "python3 phylogeny_from_mcscanx.py" if MCScanX.collinearity is available.
- convert_ncbi_idents.py can be used to convert ncbi accessions back to names like "python3 convert_ncbi_idents.py NJTree.nwk NJTree.nwk_names"
- root_NJ_tree_at_midpoint.py can be used to root the NJ trees

experimental but usually working:
- to include the elements from ../coords (see ../utils/README_utils) 
run put_coords_into_MCScanX_gff_and_homology.py and run 
{your MCScanX executable}_h -options MCScanX_plus_coords_only_relevant
like ./MCScanX_h MCScanX_plus_coords_only_relevant
- you can also run extract_MCScanX_orthologies.py afterwards to make some clusters
of elements (pretty naively from the MCScanX output collinerity file)
