Indelign is a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model.
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Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Jaebum Kim and Saurabh Sinha
Bioinformatics. 2007 Feb 1;23(3):289-97.