Sequence Alignments on the WWW or FTP

William Piel wpiel at oeb.harvard.edu
Tue May 12 18:15:25 EST 1998


In article <6ja5k0$qbk at net.bio.net>, Brian Foley <btf at t10.lanl.gov> wrote:

> I just went searching for pre-built multiple sequence
> alignments on which to test some phylogenetic software.

TreeBASE stores phylogenetic trees and datasets. About 40% of its records
contain molecular data. You can either:

* search out records individually through the web:
  (e.g., use "DNA" as a keyword) 

http://www.herbaria.harvard.edu/treebase/

* or, ftp and then browse through 250 or so files at:

ftp://www.herbaria.harvard.edu/pub/piel/Data/files/

These are in NEXUS format. Various programs can act as translators between
NEXUS and other formats. For example, MacClade will translate NEXUS into 
NBRF, SeqPup will convert between NEXUS and FASTA, NBRF, etc..

If you find this database at all useful, please consider posting your own
phylogenetic data to TreeBASE. TreeBASE accepts data from studies that are
published or "in press." 

cheers,

Bill Piel




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