Denovo repeat finder

A denovo repeat finder is a program designed to find repeats in DNA sequence without using the RepeatMasker library. Currently there are a few choices for denovo repeat programs:

• RepeatScout
• RECON
• PILER
• WindowMasker
• RAP
• orrb a very fast denovo repeat finder for alignment only

Some of these programs find repeats on their own, but some create custom libraries for RepeatMasker.

History

RepeatMasker was created a long time ago. Arian Smit was the original author but Robert Hubley is now an author as well. In 2002, RECON was created by Sean Eddy's lab at Wasington Univeristy of St. Louis. In 2005, RepeatScout and PILER were both made.

Comparing Repeat Finders

Currently there are published comparisons between RepeatScout and RECON, and also comparisons with RepeatMasker. Eventually this section will detail some experiments too.

See Also

• RepeatMasker