Improving phonetic alignment by handling secondary sequence structures

In traditional alignment analyses, sequences are only compared with regard to their primary structure. Here, the term primary structure refers to the order order of segments, whereby segments are understood as the
smallest units of a sequence which directly correspond to the characters of the alphabet from which the sequence is drawn. Apart from the primary structure, sequences can, however, also have a secondary
structure. Apart from segmentizing sequences into their primary units, one can further segmentize them into larger units of subsequences consisting of one or more primary segments. A secondary segmentation
which is very common in linguistics is, e.g., the segmentation of words into syllables apart from the primary segmentation of words into phonemes.

In the paper, a novel algorithm is presented which aligns phonetic sequences both with respect to their primary and their secondary structure.