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Fix msa phenotype and method

Workum, Dirk-Jan van requested to merge fix_MSA_phenotype_and_method into develop

Merge request for issue #49 (closed)

This merge request should fix the output of pantools msa to better specify what phenotype is used and the results of that in relation to the MSA. Also, we can use this opportunity to clean up the MSA class as well.

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