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Update CladeGrabbing.py

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Adri K. Grow 2025-07-08 07:54:58 -04:00 committed by GitHub
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Utilities/for_trees/CladeGrabbing.py
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#Dependencies: Python3, ete3, Biopython
#Inputs: A folder containing: all PTLp2 output trees and all corresponding unaligned .fasta (pre-guidance) files
#Outputs: A folder of grabbed clades and filtered unaligned fasta files
#Example: python CladeGrabbing.py --input /Path/to/trees --target Sr_rh --min_presence 20
#Example: python CladeGrabbing.py --input /Path/To/TreesandPreGuidance --target Sr_rh --min_presence 20
#IMPORTANT: key parameters explained in "add_argument" section below
#Dependencies