Figure 2
From: The ancient history of the structure of ribonuclease P and the early origins of Archaea
Fundamental steps in phylogenetic reconstruction. (A) Seven bacterial RPR sequences are randomly selected from the 133 accessions used in the present study and segments of the sequences between "..." are used to illustrate the procedure. Brackets above the sequences delimit three helical regions (P1, P2, and P12). Paired bases are marked using ">" and "<" under the sequences. (B) Complete data matrix describing the length of a total of 129 substructures derived from the annotated sequences. These substructures and their character states are described in Additional file 1: Tables S1 and S2. Substructures P1, P2, and P12 are highlighted in bold. (C) The input files in NEXUS format used to generate phylogenetic trees of substructures (left) or molecules (right) using PAUP*. The files contain the data matrices with description of characters and taxa, phylogenetic assumptions, and the hypothetical ancestral states defined by command "ANCSTATES" under the "DATA", "ASSUMPTIONS", and "PAUP" blocks. Only helical substructural characters for P1, P2 and P12 (left) and seven RPR molecules (right) are listed as taxa in the matrices.