Graphical Computation of Parameterized Alignments

Version 2.0a

XPARAL is an X-Windows based program that computes a parameterized alignment of two sequences. The user has a choice of parameterizing any two of the alignment objective function terms. These parameters include the weight of matches, mismatches, insertion s or deletions. In addition, if an linear or convex gap model is chosen, gap initiation and gap extension costs can also be parameterized. XPARAL then decomposes the two user provided input sequences according to a chosen alignment type (global, local, en d-gaps free or substring). The program will display the upper right quadrant of a two-dimensional graph, where the graph axes specify the possible values of the varying costs. The space 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 able to click on a polygon and see all of the optimal alignments for that range in the parameter space. It is also possible to save and print optimal alignments.

XPARAL's user interface

Executable versions of this program are available for the following operating systems (Mac, Linux, Unix and X windows only):

Source code for XPARAL and associated files: Source etc.
If you compile for platforms other than the ones here, please send me the executables to post here. Thanks.
XPARAL finds optimal alignments assuming either uniform scores for matches and for mismatches, or based on values from scoring tables read from a file. These scoring files are now included with XPARAL and can be selected from a pull down menu.

XPARAL also allows strings to be read in from files either singly or as aligned strings. Program documentation is available online or as a downloadable postscript document. For a translation into Romanian see
View this page in Romanian courtesy of azoft  
Dan Gusfield, gusfield@cs.ucdavis.edu

June 2001