Calculate pairwise distance for 3000 small sequences

Question

[ekal]

I have a .fasta with 3000 ascensions, each of which is 10 bases long. I need to calculate the alignment score between each pair of sequences - that's 3000^2 comparisons. Using R or python, what's the best way to go about doing this? Technical details like code snippets are particularly helpful.

Thanks!!

[Tonor]

This post has some tips and example python code: Massive Pairwise Comparison Using Biopython

[kloetzl]

This sounds like an interesting challenge for a 100 lines C program. ;)

[Macherki M E]

You can use biostrings package with R. It is samplest methode I think.see