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 quiet. 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 (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1687212), 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. Steve Bioinformatics Unit: Statistics, Modelling & Bioinformatics Department Center for Infections Health Protection Agency London UK http://www.hpa.org.uk/cfi/bioinformatics/index.htm <http://www.hpa.org.uk/cfi/bioinformatics/index.htm> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/ssml-general/attachments/20070727/76d668fd/attachment.html