I found some tips for speeding up `read.table()` [here][1], I wondered if anyone can suggest something for [read.fasta()][2], which is part of the seqinr library. Not that they're really comparable.

I have a ~6GB file.

 [1]: http://www.biostat.jhsph.edu/~rpeng/docs/R-large-tables.html
 [2]: http://www.inside-r.org/packages/cran/seqinr/docs/read.fasta
Since that function is written in R I don't think optimizing your code will result in much of a speed up compared to using a library written in another language. If you want to work in R, it would probably be easier to use the `system()` command to transform your sequences with another program or just use command line as Pierre suggested. If you have a specific task I'm sure people can provide a solution.