Variation in alignment score induced by choice of guide tree. Alignment quality scores for a collection of five test cases (a-e) taken from the HOMSTRAD/Pfam dataset, and aligned with ClustalW using guide trees generated from a variety of sources. Quality scores using guide trees from ClustalW -quicktree and from mBed are shown as arrows. Scores from 1000 randomised guide trees are shown in dark blue. Scores from 1000 SparseMap guide trees are shown in light blue.