Regarding the DNA barcode COI (cytochrome oxidase subunit 1), I'm looking for a multiple sequence alignment that, ideally, spans the Eukaryota.
Is there any such alignment available for download?
I have found tons of smaller alignments (covering, e.g., a genus) but I am kind of hoping that somebody has put together a large, taxonomically inclusive COI alignment.
You can download over 2mln Animal COX1 barcode sequences from BOLDdatabase. Unfortunately, it would require some bioinformatic work and computing power to extract, merge and align all of the sequences.
http://www.boldsystems.org/index.php/datarelease
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Barcode sequences downloadable by taxons in fasta format.
http://www.boldsystems.org/index.php/TaxBrowser_Home
Many thanks for your kind assistance! I was sort of hoping that somebody had done the bioinformatics already, but I guess I may have to do it myself.
COi sequences are not large so so simply download representative Eukaryote sequences for COI, align them and then analyse them using NJ to make sure that the sequences are informative and then do a proper maximum likelihood test.
BTW, I really think that COI barcoding is not going to reliably return good results. It is a good gene but no gene by itself can be thought to reflect the evolutionary history of going that far back in time over such diverse species. You will get an answer but the question is: do you believe it.
Hi!
I do not really know if they are useful but..If you haven't come across them yet I suggest you Damon et al. 2010 and Borriello et al. 2014..
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