|RepeatMasker Open-3-1.6 Release Notes|
As the repeat databases have grown so has the complexity of relationships between repeat families. In this version of RepeatMasker we have developed a new method for classifying and grouping related transposon fragments. The new method utilizes a set of auto-generated family-family similarity alignments to identify ambiguous fragments and their possible family associations. A new option in RepeatMasker ( -lcambig ) will identify these ambiguous fragments in the .out file with lowercase characters. All non-ambiguous fragments are labeled in uppercase. The following example illustrates how various fragments of the MER58/Cheshire subfamilies would be annotated.
Ambiguous elements may have 3 or more possible family classifications. The one chosen is based on supporting evidence from flanking annotations. In some cases there is one related non-ambiguous element which, when combined with this element uniquely identifies which family is the correct choice. For example: