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Choose some biological, medical, or environmental issue that is related to a known gene or group of genes. For example, nitrogen fixation is related to nifH/K/D/N. COVID-19 vaccines are related to viral spike proteins.
Collect at least 25 sequences of the gene, from various closely related species. Call this your “basic data set”.
Collect at least 25 sequences of the gene, from a clade that is related to the basic set. Call this your “related data set”.
Apply 123A techniques to your data to get a sense of the diversity of your chosen gene(s). Build a multiple-sequence alignment and a phylogenetic tree.
Use 80% of the sequences in your basic data set to build a Hidden Markow Model. Use 80% of the sequences in your related data set to build a HMM.
For each of the 20% of sequences that weren’t used to train an HMM, compute the log-Viterbi score on each HMM.

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