I would say: yes, you can use the program, but there maybe some alternative:

http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker

http://www.repeatmasker.org/ - some details

http://sebastien.tempel.free.fr/Boulot/UsingRepeatMasker.pdf

https://sourceforge.net/u/djinnome/jamg/ci/cdb359ae807642fef1e505c27180258d01f92f8e/tree/3rd_party/RepeatMasker/repeatmasker.help

Other tools - the alternative depends upon what exactly you need:

A field guide to whole-genome sequencing, assembly and annotation

http://onlinelibrary.wiley.com/doi/10.1111/eva.12178/full

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0654-5

http://www.cbcb.umd.edu/software/RepeatFinder/