.. _otu_comparison_tree:

.. role:: var

================================
Extension: Comparing OTU methods
================================

Now that we’ve learned a quick method of building trees, we can use this knowledge to compare our OTUs from different methods.

.. admonition:: Data
	:class: green
	
	The input data for this extension is two or more FASTA files comprising OTUs generated by different methods. If you're following along step-by-step, these would have been produced in the :ref:`OTU delimitation tutorials<otu_delim>`. Alternatively, you can use the following files from the :ref:`sectionD archive<sectionDdata>` as example data:
	
	* Greedy clustering: ``otus_greedy_0.97.fasta``
	* Linkage delimitation: ``otus_linkage_13.fasta``
	* Bayesian clustering: ``otus_crop_s.fasta``
	* Phylogenetic delimitation: ``otus_bPTP.fasta``

First, let’s create a directory for this little side project, just to be organised

Second, we need to create copies of our OTU files with names added to the headers in order to differentiate OTUs from different methods. For each OTU file, run the following command, replacing ``method`` with a description of the method used to create OTUS, e.g. ``greedy97`` (text or numbers only, no spaces or other characters!):

.. parsed-literal::
	:class: codebg

	sed -e "s/\\(^>.\*$\\)/\\1\ :var:`method`/" :var:`input.fasta` > :var:`newdirectory/output.fasta`

Next, concatenate these OTU files into one file - you’ll need to be inside your new directory for this:

.. parsed-literal::
	:class: codebg

	cat \*.fasta > :var:`output.fasta`

.. admonition:: Exercise
	
	* Run FastTree on this file, using the command from :ref:`the previous tutorial<otu_tree>`.
	* How do different OTUs match up with the different methods?