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Why do we edit sequence alignments?
What are 'hidden regions' in an alignment?
What are 'hidden regions' in an alignment?
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While algorithms can get you to/near a reasonable solution, it may not always be the best/correct. Manual inspection/editing of the alignments (since you can consider biological context e.g. presence of domains etc) can help improve the results (as long as you do the editing within reason). See this thread on BioStars for some more pointers. -
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