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.. _filter_tree:
.. index:: filter_tree.py
*filter_tree.py* -- This script prunes a tree based on a set of tip names
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**Description:**
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:** :file:`filter_tree.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_tree_filepath
Input tree filepath
-o, `-`-output_tree_filepath
Output tree filepath
**[OPTIONAL]**
-n, `-`-negate
If negate is True will remove input tips/seqs, if negate is False, will retain input tips/seqs [default: False]
-t, `-`-tips_fp
A list of tips (one tip per line) or sequence identifiers (tab-delimited lines with a seq identifier in the first field) which should be retained [default: None]
-f, `-`-fasta_fp
A fasta file where the seq ids should be retained [default: None]
**Output:**
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
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