EFFICIENCY OF ALIGNMENT PROCEDURE IN RESPECT OF RECONSTRUCTION RELIABILITY

A method is outlined which permits one to estimate the reliability of alignment procedures by comparing the real alignment obtained by gener ating appropriate sequences with the results of the alignment procedur e. The use of the method is illustrated by testing the OPAL286 program . The relation between reliability of the results (i.e. reconstruction of the real alignment) and the proportion of mutations and deletions is discussed. The proposed method provides an optimal choice of parame ters with respect to alignment reliability.