AMAS accepts command line arguments and provides a detailed textual breakdown of the conservation within a multiple alignment. Figure 4 illustrates the AMAS textual analysis that corresponds to the alignment shown in Figure 3. Only those positions that display conservation of the properties in the chosen property index are described. The presentation of the text results is hierarchical. Identities described first (1), followed by positions showing conservation of physico-chemical properties (2) , and unconserved positions listed last (3). Each entry contains a record of the alignment position (rounded brackets to the left), of the sub-groups(s) to which it refers and a list of the residues in each sub-group cited (square brackets). In addition, for positions that do not show identities, the properties conserved at the position, and those which differ are reported. With reference to Figure 4:
Identities: Section 1 lists those sequence positions that are identical across the whole alignment, between pairs of sub-groups and within one sub-group. Information is not repeated lower down the hierarchy if it has already been presented, e.g. the Gly at position 1 in the alignment is not also reported as two pairs of identical sub-groups or as three identical individual sub-groups.
Conservation of Properties: Conservation of physico-chemical properties between sub-groups (following the same redundancy rules as for identities) is reported in section 2. The four categories of conserved positions are: (1) all subgroups conserve similar properties; (2) pairs of conserved sub-groups share similar properties; (3) pairs of conserved sub-groups have dissimilar properties; and (4) individual sub-groups are conserved. The properties that are positively conserved between pairs of sub-groups are listed, as are those properties that cause differences between subgroups. For each of a pair of different sub-groups, the percentage of residues that display the differing properties is shown in square brackets.
Unconserved: There are two divisions, the first for single unconserved sub-groups and the second for entirely unconserved alignment positions.