parameter setting

[hfl112]

Hi Team member,
I am testing the TreeAlign using the data downloaded from : https://zenodo.org/records/7517412
I am using the sample SA039, I tried both tree-based and clones-based method;
For the tree-based one, I ran with default parameter:
obj = CloneAlignTree(tree=tree, expr=expr, cnv=cnv, hscn=hscn, snv_allele=snv_allele, snv=snv_total, repeat=10)
but the result is different from the output from zenodo result, even the node is different:

So how to tune the parameters ? another thing is how to map this node_number back to the newick tree?

For the clone-based result, I am encountering the same prob mentioned here:#2
I changed those two parameters to 0.6, but still got 2k+ cells not assigned

which one is more recommended? tree-based model?