A python script for identifying clusters in phylogenetic trees based on a one dimensional scanning statistic on clade branch lengths.
Requirements:
Requires python 2.x and the dendropy python library
Usage: TreeGubbins.py [options]
Options:
-h, --help, show this help message and exit
-t FILE, --tree=FILE, Input tree file (NOTE: tree must be fully bifurcating)
-o OUTPUT, --output_prefix=OUTPUT,
Output prefix
-s FLOAT, --significance=FLOAT,
Significance cutoff level [default= 0.05]
-p INT, --permutations=INT,
Number of permutations to run to test significance
[default= 100]
-m, --midpoint, Midpoint root output tree pdf [default= False]
-l LADDERISE, --ladderise=LADDERISE,
ladderise tree (choose from right or left) [default=
none]
-i, --iterative, Run in iterative mode, which allows nested clusters.
Default = do not run iteratively (much faster)
Output: The csv file produced by TreeGubbins can be viewed along with the tree in Phandango: http://www.phandango.net