A program that midpoint roots trees then calculates and reports their root-to-tip variance.
python3 RootingAndVariance.py folder_of_genes outfile_prefix
For example, using the ExampleGenes folder to create the outputs example.csv and example.log as included here, the command was:
python3 RootingAndVariance.py ExampleGenes example
The output file [outfile_prefix].csv lists the name of each file in the gene column and the corresponding root-to-tip variance, as calculated by the phyx tool pxlstr, in the root_tip_var column.
Phyx will also produce a log called phyx.logfile, and the program generates a file called temp.tre that can be deleted after running.
This program uses DendroPy to midpoint root unrooted trees and phyx to calculate root-to-tip variance.