Tools
RSPB
It's dsigned to run on a linux-like platform. The latest version of RSPB is RSPB v0.20.zip. Use this link to download the manual for RSPB. The RSPB reference is:
Lu C, Chen J, Zhang Y, Hu Q, Su W, Kuang H: Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol 2012, 29:1005-1017.
MITE-Hunter
The MITE-Hunter program can be downloaded from http://target.iplantcollaborative.org/mite_hunter.html
RepeatMasker v3.2.9
The RepeatMasker program can be downloaded from http://www.repeatmasker.org/
MITE Digger
The MITE Digger program can be downloaded from http://labs.csb.utoronto.ca/yang/
Other software required by RSPB:
BLAST ftp://ftp.ncbi.nih.gov/blast/executables/release/
Muscle http://www.drive5.com/muscle/
Mdust http://compbio.dfci.harvard.edu/tgi/software/