How to generate it - How to generate it? How do we generate...

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How to generate it? How do we generate a multiple alignment? There is an obvious solution: Given a pairwise alignment, just add the third, then the fourth, and so on , until all have been aligned. But is this as straightforward as it looks? Consider a case with three short fake sequence that are pair-wise homologous in the following way: dront ...AGAC. .. t-rex ...--AC. .. dront ...AGAC. .. unicorn . ..AG--. .. t-rex ...AC. .. unicorn . ..AG. .. It is not self-evident how these sequences are to be aligned together. Here are some possibilities: dront ...AGAC. .. t-rex ...--AC. .. unicorn . ..AG--. .. dront ...AGAC. .. t-rex ...AC--. .. unicorn . ..AG--. .. dront ...AGAC. .. t-rex ...--AC. .. unicorn . ..--AG. .. A multiple alignment depends in a non-trivial way on the various parameters (insertion/deletion penalties, substitution coefficients,. ..), and, importantly, also on the order in which sequences are added to the growing multiple alignment. In pairwise alignments, one has a two-dimensional matrix with the sequences on each
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How to generate it - How to generate it? How do we generate...

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