This is more just a pet-peeve and not that important. Currently, the ladderize! command will change the order of leaves in mcc clades if they have the same rank in the tree, which is quite confusing. For example:
nwk_1 = "(A,(B,C,D,E))"
will become
nwk_1_ladderize_output= "(A,(E,D,C,B))"
after calling ladderize! on the tree.
I found this quite confusing. I initially just wanted nodes to stay the same as in input order but think it might be even nicer if we are anyways sorting them to sort the nodes of same rank in a polytomy by alphabetical order.
I have added a small test. Additionally, I tested it on the NY data set in TreeKnit to make sure this works on large trees.
This is more just a pet-peeve and not that important. Currently, the
ladderize!command will change the order of leaves in mcc clades if they have the same rank in the tree, which is quite confusing. For example:nwk_1 = "(A,(B,C,D,E))"will becomenwk_1_ladderize_output= "(A,(E,D,C,B))"after callingladderize!on the tree.I found this quite confusing. I initially just wanted nodes to stay the same as in input order but think it might be even nicer if we are anyways sorting them to sort the nodes of same rank in a polytomy by alphabetical order.
I have added a small test. Additionally, I tested it on the NY data set in
TreeKnitto make sure this works on large trees.