SPLISO is described in the paper "Site-directed combinatorial construction of chimaeric genes: General method for optimizing assembly of gene fragments", by L. Saftalov, P.A. Smith, A.M. Friedman, and C. Bailey-Kellogg, Proteins, 2006, 64:629-642. This web-based demonstration version is limited in terms of the number and length of sequences, the number of breakpoints, and the substitution and shift models, as described in the form below. The full, unrestricted Java code may be obtained for academic use by contacting Chris Bailey-Kellogg.

The default example is the N-terminal portion of TEM-1 and PSE-4, from the paper; try as is vs. with substitutions or shifts.

Multiple sequence alignment
up to 5 rows by 100 columns (amino acids and gaps)
up to 5 comma-separated positions (each on the N-terminal side of the breakpoint location)
Allow substitutions?
ΔBLOSUM ≤ 4, at that penalty
Allow shifts?
± 1 position, at penalty of 1