If you use "-alrt" and "-bb" in iqtree, you will get "90/100" like bootstrap value in the tree file. This program let you choose which value to keep, SH-like aLRT test value (use option "-1" or "--alrt") or Ultrafast bootstrap value (by default).
python3 remove_alrt_value.py input_treefile
- "-o" Set output filename. The default is "old_filename.new".
- "-1" or "--alrt" Keep SH-like aLRT value instead.
This program assumes that your iqtree option is "-alrt -bb", i.e., Ultrafast bootstrap value is the second. If you change the order, then you have to change option.
Collapse clade which have too short branch or too long branch or too low confidence.
python3 collapse.py input.nwk -lmin 0.001 -lmax 0.5 -bmin 50 -draw
If set "-draw", it will generate picture for you to view interactively.
Parameters:
-
lmin: minimum branch length -
lmax: maximum branch length -
bmin: minimum confidence of the clade
The output contains two files:
- input.collapse collapsed tree as phyloxml format
- input.xml original tree with colored branch that red means short branch, green means long branch, blue means low confidence clade.
It is recommend to use Archaeopteryx to view phyloxml format tree file.
python3 collapse.py tree.nwk -lmin 0.002 -lmax 0.3 -bin 90