[ssml] Standard for comparing nucleotide alignments

[paul.boutros at utoronto.ca]

Hello,

I am looking for some sort of a "basis" set for comparison of nucleotide 
alignment software/algorithms/scoring systems.  Essentially, I am looking for 
the equivalent of BAliBASE for nucleotides: a set of validated alignments of 
varying distances that I can trust.

The original paper for BAliBASE was:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
cmd=Retrieve&db=PubMed&list_uids=11125126&dopt=Abstract

Ultimately, I would simply like to have an objective way of comparing different 
pairwise nucleotide alignment systems.  I do realize the difficulties involved 
in comparing non-coding vs. coding sequence, but I have not found a suitable 
basis set for either case.

Any suggestions or ideas are very much appreciated!
Paul