1. A method for conducting an optimal treatment protocol selection and determining case progression by executing computer-executable instructions stored on a non-transitory computer-readable medium, the method comprises the steps of: providing a plurality of searchable cases stored within a database, wherein the database is a knowledge base; receiving a plurality of new clinical experiences, wherein each of the plurality of new clinical experiences comprises a plurality of nucleotide sequences, a plurality of amino acid sequences, a clinical information set, a treatment protocol, and a treatment outcome; creating new searchable cases from the plurality of new clinical experiences by way of a case creation method; indexing the new searchable cases and the plurality of searchable cases; organizing the plurality of searchable cases for facilitated retrieval and analysis, wherein the searchable cases comprise a sequence analysis case and a combined clinical and sequence analysis case; wherein the sequence analysis case and the combined clinical and sequence analysis case each comprise a provided sequence, a reference sequence, and a mutation set; wherein the combined clinical and sequence analysis case further comprises a clinical information set, a treatment protocol, and a treatment outcome; performing a sequence analysis on the plurality of new clinical experiences by way of a sequence alignment algorithm; and selecting a treatment protocol based on the plurality of new clinical experiences by performing an optimal treatment selection method.