Created
April 13, 2018 18:54
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A script for counting the total species in each clade in a Newick formatted file.
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| # Michael A. Alcorn | |
| from Bio import Phylo | |
| tree = Phylo.read("species_newick.txt", "newick") | |
| clade_counts = {} | |
| for clade in tree.find_clades(): | |
| if not clade.is_terminal(): | |
| clade_counts[str(clade)] = clade.count_terminals() | |
| clade_counts = list(clade_counts.items()) | |
| clade_counts.sort(key = lambda x: -x[1]) |
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