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This script takes a tree and a list of OTU IDs (in one of several supported formats) and outputs a subtree retaining only the tips on the tree which are found in the inputted list of OTUs (or not found, if the –negate option is provided).
Usage: filter_tree.py [options]
Output is a pruned tree in newick format.
Prune a tree to include only the tips in tips_to_keep.txt:
filter_tree.py -i rep_seqs.tre -t tips_to_keep.txt -o pruned.tre
Prune a tree to remove the tips in tips_to_remove.txt. Note that the -n/–negate option must be passed for this functionality:
filter_tree.py -i rep_seqs.tre -t tips_to_keep.txt -o negated.tre -n
Prune a tree to include only the tips found in the fasta file provided:
filter_tree.py -i rep_seqs.tre -f fast_f.fna -o pruned_fast.tre