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This script computes from an OTU table a matrix with the number of shared phylotypes between all pairs of samples.
Usage: shared_phylotypes.py [options]
Compute shared OTUs on one OTU table for all samples
shared_phylotypes.py -i otu_table.biom -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.biom -o shared_otus_PC.636.txt -r PC.636
Batch mode example:
Compute shared OTUs for a set of OTU tables, e.g. from running multiple_rarefactions.py, with an even number of sequences per sample. The resulting directory can be fed to dissimilarity_mtx_stats.py, which computes mean, median and the standard deviation on the provided tables.
shared_phylotypes.py -i rarefied_otu_tables/ -o shared_otus/
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