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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:

(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 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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