Can anybody guide how a perfect alignment is obtained or constructed which can be compared with balibase alignment with baliscore? If we consider total conserved column score then it is possible to get lesser sum of pair score, whereas for a good sum of pair score we may possible to get lesser number of conserved columns. How the alignment is optimized based on evolutionary algorithm where fitter alignments are selected for the next iteration.
Ahmed Abdo
there are many algorithms are used to optimize the score of the alignment. for example Genetic algorithm.. It selects best alignment to be parent for generating childrens. There is a package called SAGA. you can use it or read the paper
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