Sequence Alignments on the WWW or FTP

Dr. Andrew G. McArthur mcarthur at
Tue May 12 16:24:50 EST 1998

Take a look at:

D.R. Maddison, D.L. Swofford, W.P. Maddison. 1997. NEXUS: an extensible
file format for systematic information. Systematic Biology, 46(4): 590-621.

At 12:38 PM 5/12/98 -0600, you wrote:
>Dear molecualr evolutionists,
>	I just went searching for pre-built multiple sequence
>alignments on which to test some phylogenetic software.
>	I found quite a few sets available on the WWW 
>by searching YAHOO (  for 
>"multiple sequence alignment".  However, I did not find
>the same format at each site, and most sites provided
>text formats from which comments and annotations needed
>to be removed prior to re-formating for analysis.
>	It would be a huge help, if we could all agree
>on a format (such as FASTA format) that could be saved
>and retrieved for analysis, as well as the text formats for 
>human reading or printing.
>	At the HIV Database, we try to provide both text
>and more machine-readable formats for our alignments.  
>Is FASTA format the "industry standard" or are there reasons
>to use another format?
> ____________________________________________________________________
>|Brian T. Foley               btf at                       |
>|HIV Database                 (505) 665-1970                         |
>|Los Alamos National Lab     |
>|Los Alamos, NM 87544  U.S.A. |

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