Table of Contents
-----------------

-  `What is repmsa? <#what-is-repmsa>`__
-  `Installation <#installation>`__
-  `Usage <#usage>`__

What is repmsa?
---------------

Creating a percentage identity matrix from a multiple sequence alignment
and then ranking them to select the best sequence representetive in the
Multiple Sequence Alignment. repmsa ranks the sequences based on highest
identity.

Installation
------------

``pip install repmsa``

Usage
-----

.. code:: python

    from repmsa import RankMatrix
    var = RankMatrix(msa_file)
    print(var.dm) #prints the distance matrix
    df #prints the distance matrix in data frame.
    var.id_iter #is the iterator from highest ranked to lowest rank.
    var.ranked #returns the ranked list in a listed tuple.
    var.topids() # returns the id of the highest ranked sequence, each time its called it moves the next highest one.
    var.seq_by_id('QIQ56215.1') # returns the sequence by the id that is provided.
