Fig. 3

MSAs inferred with PRANK+F (top), our algorithm (middle, denoted by P-PIP) and MAFFT (bottom) from 23 strains of gp120 human and simian immunodeficiency virus (always using the same guide-tree). a. The total MSA lengths are 669, 661 and 579 columns respectively. The three methods show good agreement in the conserved regions. Substantial differences are observed in regions 1–4, highlighted by colors. b. Magnification of Region 4. MAFFT over-aligns the sequences. Depicted on the left: The tree in black is the original guide-tree. The trees depicted in colour are the same guide tree but with re-estimated branch lengths. A detailed view of regions 1–3 is given in Additional file 1: Figures S1-S3