Figure 2
From: Scoredist: A simple and robust protein sequence distance estimator
The Belvu multiple sequence alignment viewer. Belvu is a multiple sequence alignment viewer that implements the Scoredist distance estimator. The alignment window (A) shows a subset of the Pfam family DNA_pol_A (PF00476). Uniprot IDs are shown throughout. A sequence with known structure is included (DPO1_ECOLI) – the SA line showing surface accessibility and the SS line showing secondary structure. The neighbour-joining tree in (B) used uncorrected distances (observed differences), while the tree in (C) used Scoredist correction. Belvu assigns a colour to each species if provided with species markup information. The distance correction mainly affects the longer branches, and affects the tree topology in some cases, e.g. the placement of DPOQ_HUMAN. Structural markup and taxonomic information were embedded in the Stockholm format alignment provided by the Pfam database.