XPARAL
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.
Version 2.0 is both faster and more robust. It also has the added feature of being able to choose from three gap alignment models: affine, logarithmic, or square root. Click here to find out more about gaps in XPARAL.
Executable versions of this program are available for the
following machines (Linux, Unix and X windows only):
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.
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Click here to get a sample file of aligned strings.
Program documentation is available online or as a downloadable postscript document.
Currently maintained by CS Support for:
Dan Gusfield, gusfield@cs.ucdavis.edu
June 2001