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.. _shared_phylotypes:
.. index:: shared_phylotypes.py
*shared_phylotypes.py* -- Compute shared OTUs between all pairs of samples
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script computes from an OTU table a matrix with the number of shared phylotypes between all pairs of samples.
**Usage:** :file:`shared_phylotypes.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-otu_table_fp
Path to the input OTU table or a directory containing (only) OTU tables
-o, `-`-output_fp
The output filepath
**[OPTIONAL]**
-r, `-`-reference_sample
Name of reference sample to which all pairs of samples should be compared [default: None]
-f, `-`-force_overwrite
Overwrite output_fp if already exists [default: None]
**Output:**
**Single file example:**
Compute shared OTUs on one OTU table
::
shared_phylotypes.py -i otu_table.txt -o shared_otus.txt
**Reference sample example:**
Compute shared OTUs with respect to a reference sample. Computes shared OTUs between all pairs of samples and the reference sample. E.g. in a transplant study this can be used to establish a base line count of shared OTUs with the Donor sample before and after the transplant.
::
shared_phylotypes.py -i otu_table.txt -o shared_otus.txt -r Sample_X
**Batch mode example:**
Compute shared OTUs for a set of OTU tables, e.g. from running `multiple_rarefactions.py <./multiple_rarefactions.html>`_, with an even number of sequences per sample. The resulting directory can be fed to `dissimilarity_mtx_stats.py <./dissimilarity_mtx_stats.html>`_, which computes mean, median and the standard deviation on the provided tables.
::
shared_phylotypes.py -i rarefaction_out/ -o rarefied_shared_otus/
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