[ssml] Assess sequence alignment quality without reference alignments?

Steven Platt Steven.Platt at HPA.org.uk
Fri Jul 27 06:32:01 EDT 2007

Is this list still active? I've not heard anything here since the end of
last year, but hey... maybe we all know what we need and have kept
Serious question:
Is there an algorithm / method / program or server that can assess the
quality of a nucleotide multiple sequence alignment (generated by a
progressive clustering algorithm e.g. Clustal), without the need for a
reference alignment? 
I've come across several papers & servers via Google & PubMed but all
need reference alignments or are for protein sequences where structural
information is available. The closest so far is by Ahola et al
which looks great until you reach the end of the alignment quality
section of the methods and find the sentence 'By comparing the ConsAAs
calculated from the test and reference alignments...'. 
The ability to bootstrap trees generated from alignments is already well
established and I'd like to get some thing that examines the alignment
more directly.
What I'm really looking for is a method that I can apply directly to the
alignments generated by our users that is better than a simple set of
column conservation scores across the alignment ... but I'm starting to
think that such a thing does not exist.
Any advice would be helpful.
Bioinformatics Unit: Statistics, Modelling & Bioinformatics Department
Center for Infections
Health Protection Agency
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