Add ResidueSubstitutionMatrices module

[diegozea]

Summary

• add new ResidueSubstitutionMatrices submodule under MIToS.MSA
• implement ResidueSubstitutionMatrix type and indexing
• export new module from MSA
• add tests for the new type
• refine ResidueSubstitutionMatrix defaults and pretty printing
• split getindex into separate Int and Residue methods
• refine AbstractArray interface of ResidueSubstitutionMatrix
• use alphabet type parameter and remove custom IndexStyle

Testing

• julia --project -e 'push!(LOAD_PATH, "test"); using MIToSTests; MIToSTests.retest("MSA"); MIToSTests.retest("ResidueSubstitutionMatrices")'

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https://chatgpt.com/codex/tasks/task_b_6848ba49d4f0832da11a9122d839b3bb