XPARAL is an X-Windows based program which computes a parameterized alignment of two sequences, displaying all of the optimal alignments for the two sequences when the costs of substitutions, gaps and insertions or deletions are varied. The user provides as input two sequences, an alignment type (global, local, end-gap free and substring), and selects which two of the alignment costs to vary. The program then displays the upper right quadrant of a two-dimensional graph, where the graph axes specify the possible values of the varying costs. The quadrant is partitioned into convex polygons, where each polygon specifies an alignment that is optimal over the range of costs within the polygon. The user is then able to view and print out those optimal alignments.
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Methods Enzymol. 1996;266:481-94.
Parametric and inverse-parametric sequence alignment with XPARAL.
Gusfield D, Stelling P.