Table 1.
The 8,362 Optimal Alignments for Two Drosophila Intron Sequences
Figure 1.
The Alignment Polygon for Our Two Introns Is Shown on the Left
For each of the alignment summaries A,B, . . . F in Table 1, the corresponding cone in the alignment fan is shown on the right. If the parameters (S,X) stay inside a particular cone, every optimal alignment has the same alignment summary.
Figure 2.
The Jukes–Cantor Matrix, Kimura-2 Matrix, and Kimura-3 Matrix
These three matrices correspond to JC69, K80, and K81 in the Felsenstein hierarchy [11] of probabilistic models for DNA sequence evolution.
Table 2.
Face Numbers of the Alignment Polytopes for the Intron Sequences from the Beginning of the Introduction
Figure 3.
The Third Alignment Polytope of Our Two Drosophila Introns Has 76 Vertices
The marked vertex (x,s,g) = (30,5,2) represents the BLASTZ alignment.
Table 3.
Observed Running Times of the Incremental Convex Hull Algorithm for Computing Alignment Polytopes
Table 4.
Averages of the Number V of Vertices and the Number F of Facets of Alignment Polytopes
Table 5.
Cis-Regulatory Element Conservation
Figure 4.
The Jukes–Cantor Distance Function of Two Drosophila Genomes