question about scoring a multiple sequence alignment 7-21-14

2014-08-29

question about scoring a multiple sequence alignment 7-21-14
score msa

email
https://mail.google.com/mail/u/0/?ui=2&shva=1#search/hamish/147582100da767ff 





Hi,





> Is there a way that I can view a single quantitative score that


> indicates the quality of a multiple sequence alignment in Clustal


> Omega?  If there is not, perhaps I could quickly calculate it from the


> resulting output matrix?  Thanks for any help and information you have


> to offer!





Assessing alignment quality is an active area of research. I suggest you search the web and the literature for possible tools and try them on your alignment to assess which will work for your case. See:





https://www.google.com/search?q=alignment+quality+score


http://europepmc.org/search?query=multiple%20alignment%20quality%20score





All the best,





Support@EMBL-EBI



Note that later on I found the following page which describes some methods for scoring a multiple alignment 


-scoring functions


--minimum entropy


--sum of pairs