Hi Steve, Such a thing most definitely exist, at least for protein sequences. I'm not sure exactly what you are looking for because you ask for the assessment of _nucleotide_ multiple sequence alignments, yet below you gave an example for protein multiple alignments. Either way, type Poch O or Thompson JD (better yet, both) into PubMed and you will have plenty to read. In particular, look at articles with PMID numbers 11734009 and 12801878 or just type "norMD align" into any search engine. SAM ( http://www.soe.ucsc.edu/compbio/sam.html ) has a function that improves the existing alignments of _protein_ sequences while removing unrelated entries, but it is fairly slow. Finally, if you are looking only for nucleotide alignments, as stated, I suggest you contact the experts directly - Oliver Poch and Julie Thompson certainly come to mind. Best regards, Mensur At 04:32 AM 7/27/2007, you wrote: >Content-class: urn:content-classes:message >Content-Type: multipart/alternative; >boundary="----_=_NextPart_001_01C7D039.5E9D2F84" > >--> > >Is this list still active? Ive 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? > > > >Ive 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>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 Id like to get some thing that examines the alignment >more directly. > > > >What Im 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 Im 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 > > >_______________________________________________ >ssml-general mailing list >ssml-general at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/ssml-general ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic at montana.edu | ==========================================================================