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Usearch will do all-against-all comparisons, cluster sequences, and produce alignments for each cluster. You can set the clustering threshold (proportion of residues identical). The alignments are in fasta format, which is pretty standard. If all you want is basic similarity it might be easiest to just write something that calculates normalized Hamming distances (typically called p-distances in the molecular evolution literature) between pairs of sequences. I suspect the biopython fasta reader (you can install biopython from https://biopython.org/) will be good enough.
Diamond (https://github.com/bbuchfink/diamond) might help. It has a protein sequence clustering option. You could cluster your sequences and then take the centroids of each cluster. Vary the BLAST parameters to increase/decrease the numbers of clusters.