Which is the MULTIPLE ALIGNMENT code that can be INTERFACED most EASILY ?

Don Gilbert gilbertd at chipmunk.bio.indiana.edu
Fri Aug 1 03:09:27 EST 1997

Ouch.  But a valid criticism.  I have always cautioned SeqPup has
bugs, and wasn't ready for those who aren't willing to deal with some
hassles.  Results have varied -- some find it a helpful program,
and not as prone to crashing as others do.  I'm sorry to hear
that some people find it too crash-prone to be useful.

One of the more frustrating aspects of developing
this program with its current (old) platform-independent framework 
is/was the difficulty of tracking down and squashing those frustrating, 
often very computer system specific bugs.

That is one main reason I'm now moving it from a C++/NCBI-toolkit
framework to a Java framework.  Java programs are easier to make
bug-free, and less likely to have platform-specific problems.
Look for a pre-pre-pre-alpha of the java version soon (it may
in fact be usable w/o crashing, but won't have all the features
of the current c++ version, but may have some new ones).

As an aside on the main topic of this news, it continues to be 
goal of SeqPup that it should easily interface w/ other biocomputing apps.
It (as the earlier SeqApp) was one of the first to provide an interface 
between clustal, cap, dnaml, and others and a graphic user interface 
biosequence editor.  This isn't an easy general goal to reach 
(esp. for multiple OSes). There may be more promise w/ a Java version, 
but it will be a while longer till the easy interfacing aspects are 
worked out.

-- Don

P.S., SeqPup is a free, source-included, multi-computer-platform 
(Mac/MSWin/XWin) biosequence editor that is found at 
The sometime to be released java version will be found there and in
the ftp://iubio.bio.indiana.edu/molbio/java/ folder also.

Mike Noren (ev-michael at SPAMSTOPnrm.se) wrote:
: SeqPup: Avoid at all cost until the programmer has got the program
: past pre-alpha stage, so that it can actually do something without
: crashing.

-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu

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