Figure 2
From: Genomic multiple sequence alignments: refinement using a genetic algorithm
Improvement of COFFEE score for fuzzy regions. The 200 fuzzy regions derived from the starting Orthopoxvirus alignment that showed improvement following application of GenAlignRefine are displayed. For clarity, regions are sorted according to the overall improvement in COFFEE score. Vertical bars connect dots that show the improvement in COFFEE score for each region at each step in the refinement process. Red dots plot the original COFFEE score of the Multi-LAGAN-generated alignment for each region; green dots plot the COFFEE score of the same region after realignment by T-Coffee; blue dots indicate the COFFEE score of the same region after optimization by the genetic algorithm. The small magenta squares plot the overall improvement in COFFEE score for each region.