clean_raxml_parsimony_tree.rst

clean_raxml_parsimony_tree.py

clean_raxml_parsimony_tree.py -- Remove duplicate tips from Raxml Tree

Description:

This script allows the user to remove specific duplicate tips from a Raxml tree.

Usage: clean_raxml_parsimony_tree.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_tree

The input raxml parsimony tree

-t, --tips_to_keep

The input tips to score and retain (comma-separated list)

-o, --output_fp

The output filepath

[OPTIONAL]

-s, --scoring_method

The scoring method either depth or numtips [default: depth]

Output:

Example (depth):

For this case the user can pass in input Raxml tree, duplicate tips, and define an output filepath. When using the depth option, only the deepest replicate is kept.

clean_raxml_parsimony_tree.py -i raxml_v730_final_placement.tre -t 6 -o raxml_v730_final_placement_depth.tre

Example (numtips):

For this case the user can pass in input Raxml tree, duplicate tips, and define an output filepath. When using the numtips option, the replicate with the fewest siblings is kept.

clean_raxml_parsimony_tree.py -i raxml_v730_final_placement.tre -t 6 -o raxml_v730_final_placement_numtips.tre -s numtips