How to Multiply Align Sequences

Multiple Alignment Accuracy - Pairwise Alignment Accuracy 

Automatic alignment programs such as CLUSTAL W (Thompson et al 1994) will give good quality aligmnents for sequences that are more than 6o- similar (Barton 

CREATION AND ANALYSIS OF PROTEIN MULTIPLE SEQUENCE ALIGNMENTS 

ALSCRIPT provides a few commands for calculating residue conservation across a family of sequences and coloring the alignment accordingly. However, it is really intended as a display tool for multiple alignments rather than an analysis tool. In contrast, AMAS (Analysis of Multiply Aligned Sequences Livingstone and Barton, 

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