Analyzing and Modifying the PRESCOTT Output
==========================================

Raw PRESCOTT Scores and Their Interpretation
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There is not a hardcoded limit for raw PRESCOTT scores. However, the values
range between [-12, 2] generally. The lower values mean the mutations is impactful, 
while values close to 0 means the mutation does not have any significant impact.

We should note that most of the 'impactful' mutations are deleterious but 
it is not always the case. 

Entire Single Point Mutation Landscape Calculations
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By default, PRESCOTT will only output the combined (independent
and epistatic) scores*: 

There are three output files:

#. myProt_normPred_evolCombi.txt

    myProt is the short name in the MSA file for your protein. The 
    'myProt_normPred_evolCombi.txt' file contains 20 rows (for 20 amino acids 
    in alphabetical order) and L columns, where L is the number of amino acids 
    in your protein of interest. Since this file is horizontal, it is easy to 
    read it in R or Python but difficult to find the mutations you are interested.

#. myProt_normPred_evolCombiTransposed.txt 

    As the name implies, this is the transposed version of the combined results.
    It is easier to find the mutations you are interested in this file. Just 
    check the row corresponding to the mutation.

#. myProt_normPred_evolCombi.png

    This is the image file of the combined results. It selects 'Oranges_r'
    matplotlib color map by default. You can change it by adding '--colormap turbo_r'
    for a more fancy look during the esgemme call. It --colormap argument accepts
    all the color maps in matplotlib.

Note*: If you want to see epistatic and independent contributions as well, 
you should add '--verbose true' argument while calling esgemme. 

Selected Single Point or Multiple Point Mutation Calculations
-------------------------------------------------------------

Since you used a mutation file to predict mutations, you will have your combined (epistatic+independent) 
results in the same format, such as :

*. myProt_normPred_evolCombi.txt:
    A2C -6.23
    A2D -1.23
    .
    .
    .
    D286F -0.23




