Figure 10

Sensitivity of homology assessment to the morphological matrices. Sequences from the D3 region ranging from helix H628 to D3_2 of two Acariformes mites (Arrenurus and Schusteria), Anactinotrichda (Amblyoma) and Solifugae (Eremobates). A- Partially aligned sequences, with regions aligned according to the secondary structure shaded blue. Parenthesis indicates pairing sites, dots unpaired sites and (*) indicates regions considered unaligned. Note that D3_1 is absent in Acariformes. B- Implied alignment bound to the best trees of the unconstrained analysis of molecular data combined with matrix A, under cost regime 1:1:1. C- Implied alignment, under the same cost regime, analysis combined with the matrix B.