Fig. 2

Overalignment example block #1. This figure shows the true MSA (top) obtained as described in section Results, the alignment obtained with MAFFT (middle), and with ProPIP (bottom). The 3 MSAs represent a portion of the entire alignment, namely columns 1–116, 1–107, and 1–114 for true, MAFFT, and ProPIP, respectively. For ProPIP we selected the MSA with the highest likelihood and not the one with the best Q score [20]. It can be noted that MAFFT tends to over-align, while the gap pattern resulting from ProPIP is more compatible with the true MSA. The similarity value (AlignStat v1.3.1 [19]) are \(75\%\) for MAFFT and \(82\%\) for ProPIP [27]. Column by column similarity values are shown under true MSA for both aligners