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
If you have a huge file (just reread your post, 6Gb), the best way is to use an index (this is how databases work...). Take a look at this link: http://stackoverflow.com/questions/23173215/how-to-subset-sequences-in-fasta-file-based-on-sequence-id-or-name

It depends on what you want to do; do you only need a subset of these sequences at any given time or do you require every one of them? You would need a way to load and store them in your RAM, rather than reading a 6Gb file each time you tinker your file. NB: you can increase R's memory to avoid errors.