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Alignment software

Anders Gorm Pedersen gorm at cbs.dtu.dk
Wed Jun 21 05:23:00 EST 2000


Brian wrote:

> I am looking for a shareware/freeware program for the macintosh which will
> be able to use editseq files generated from the DNAstar programs EditSeq and
> Seqman for alignment purposes.  If there is a program that will do this,
> will it also save the alignment in NEXUS format?  I am hoping to do more
> work from my home computer and can't afford my personal copy of the DNAStar
> tools, unless someone has a free copy they can give me.

Brian - 

I believe both Editseq and Seqman will export sequences in formats that
are understood by most alignment programs (relevant formats include:
fasta, GCG, genbank).

One excellent free alignment tool is ClustalX which is also available
for the (power?)Mac:

ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ 
(you want the file "clustalx1.81.PPC.sea.Hqx")

The program "readseq" will convert between different file formats
(including Nexus/PAUP) and is also available for the Mac:

http://iubio.bio.indiana.edu/soft/molbio/mac/ (in the file "readseq.hqx"
- there are lots of other good programs for the mac here).

Hope this helps!

Anders


---------------------------------------------------------------
 Anders Gorm Pedersen, cand.scient., Ph.D.  (gorm at cbs.dtu.dk)

 Center for Biological Sequence Analysis
 Technical University of Denmark
 Bldg 208, DK-2800 Lyngby, Denmark

 phone: (+45) 45 25 24 84
 fax:   (+45) 45 93 15 85

 Web: http://www.cbs.dtu.dk/gorm/
---------------------------------------------------------------








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