alignment editor and more, very useful!

Arthur Schuessler schueslr at sun0.urz.uni-heidelberg.de
Thu Feb 27 13:50:04 EST 1997

Dear "sequence aligners",

I want to recommend a DNA/RNA and protein alignment editor.

The program was written by a friend of mine (I "cooperated" in testing
it) during the last two years. It is for PC (Win3.x, Win95/NT). Two
Versions are available, one 16 and one 32 bit. The 16bit version can be
tested as a demo version available in WWW (see below), it runs very well
under Win3.1x and Win95. 
It is not for free, he takes 100 $ US for it now, but I think it is one
of the best (for me it's the best) alignment editors available. It will
probably become more expensive after some month. It also handles protein
sequences and is fully color coded. It is not only for alignment, but
also searches for restriction sites, makes consensus sequences,
statistics, and so on. It has comfortable features, like search and
replace nucleotides (e.g. T->U), making masks and replace non masked
regions, translation DNA or RNA -> Protein, RNA <-> DNA, showing
open reading frames, codon usage can be edited, and so on. One also can
easyly include secondary structure elements in the alignment - they can
be removed again for analysis.
>>>>>>>> I have no commercial interest <<<<<<<< - I'm just informing you. 
The adress and e-mail etc. of Dominik Hepperle (he wrote the programme)
is shown in the DEMO-version available at the WWW adress given below.
This version can >not< save files (the programm is not for free), all
other features can be tested. It handles e.g. PAUP, PHYLIP and MEGA
It is really a good programm!
It has no problems with lets say 1000 LSU rRNAs (the number is only
dependent on the memory you have). I aligned 80 fungal SSU rRNAs (about
2000 sites) with the program easyly on a 486/33 PC with 8 MB RAM (my old
private computer!). I didn't try how many are possible! probably much
The program was written during the last 2-3 years, I use it since about
one year. All serious bugs are fixed, it makes no problems and is very
stable. He had to buy the programming software and spent much time in
it, 100$ are not very much. 
But, just try it.

WWW adress:


PS: he is all the time implementing new features in the program, so if
there are suggestions or special needs from you or others, he simply
will include them, if possible (most is possible). E.g. special data
formats can be included, if needed.

Dr. Arthur Schuessler
University of Heidelberg 
Im Neuenheimer Feld 230
D-69120 Heidelberg
E-mail: schueslr at sun0.urz.uni-heidelberg.de
FAX: 06221 / 54 49 13

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