A new version of RepeatMasker is available for download. Included in
this new release are several major improvements:
- The repeat database is updated with 694 new entries and 147 improvements on
existing ones, including RepBase version 11.06. Major advances were for
ancient mammalian repeats, which are shared by all mammals or all
eutherians, and for marsupial repeats, especially for the opossum. Other
significant additions were for Chlamydomonas and Caenorhabditis briggsae.
- The annotation of DNA Transposon fragments has been improved. A new method
of joining related transposon fragments improves classification of ambiguous
fragments. More details here
- A new option ( -lcambig ) identifies DNA Transposon annotations which without
any supporting evidence are ambiguously defined. i.e The fragment falls within a
non-unique portion of the family consensus. When this option is used all ambiguous
repeat names are printed in lower case while the rest are in uppercase.
- Fixed a bug with fasta files containing more than 60MB of sequence on a single
- Updated the taxonomy database and added the "-tree" option to the queryRepeatDatabase.pl
script. The new option prints out the taxonomic tree of all species contained in the
RepeatMasker database with information on the number of repeat families defined at
- Several bugs have been fixed in the DateRepeats routine, which played when
large numbers were involved (e.g. analysis of whole chromosome RepeatMasker
output) and/or the input is a concatenation of RepeatMasker outputs (repeat
IDs are not necessarily unique anymore).
- Other improvements in DateRepeats are better labeling of ambiguously called
repeats, correctly assignment of lineage specificity to some elements that
have independently inserted in separate lineages of mammals, and refinements
in the phylogeny.