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Multiple Sequence Alignment
Pitfalls
Progressive alignment errors propagate: Early misalignments are locked in. MAFFT iterative refinement and T-Coffee's library approach mitigate this.
Tool selection by dataset size: ClustalW is O(N^2), slow beyond ~200 seqs. MUSCLE handles ~1K seqs. MAFFT --auto scales to tens of thousands; --parttree for >100K. T-Coffee is highest quality but too slow beyond ~500.
Gap treatment: Columns with >50% gaps are unreliable -- mask with t
[Description truncada. Veja o README completo no GitHub.]
