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I tried to find sources that explain multiple sequence alignment with an example using progressive alignment, but I couldn't find one.

I actually know till creating a guide tree, after creating a guide tree we use guide tree to arrange sequences. This is the critical part. Can some please help me in explaining how to align sequences that are already aligned with a new sequence.

For Example there are 5 sequences S1, S2, S3,S4 and S5. After aligning S1 and S3, suppose the aligned sequence is A1. Now the problem is I don't know how to align A1 with S2 or S4 or S5.

Please help me by explaining that with an example. Your help is much appreciated.

Thanks, Ravi

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