Nexus

[Gregor Hagedorn]

Susan Farmer wrote:
> I (initially) put all of my data into
> DELTA and then converted it to Nexus. The Nexus file has been heavily
> modified (and many of my character and state names truncated in the
> bargin).  Until very recently, there was no way to take *this* file
> back into DELTA.  But more than that; all of the continuous data
> in the original file (aka measurements) are now gone and will have to
> be added back into the DELTA data set by hand.  :-(

We had several comments on NEXUS so far.

I agree with Kevin (and Leigh), that "users of NEXUS are more than happy
with their format". However, I don't think they should be, exactly because
the situation Susan is commenting on. NEXUS is by far more specialized and
that much information is lost when restricting a data set to NEXUS. If
NEXUS does not change, it would sooner or later become a one-way format,
and would not be used for data storage any more.

That does not mean that NEXUS is not a good format, but I believe we do
need a format that is covering all the common ground. We should try to
learn from NEXUS as we should try to learn from DELTA.

>Given this, and other similar comments on the list, I'd suggest that an
>additional requirement of any new format (if thats the way things go)
>is that it provides backwards-compatibility, as far as possible with
>other formats.

I believe this backward compatibility will be possible, at least in a one-
way situation. With this I mean that a simple XML program (given the new
program is based on XML) will be able to provide DELTA or NEXUS formatted,
that can be read by older programs.

However, if the new format is really a redesign and not just a superset of
competing directives, some information may be lost, and some information
may have to be mapped in a way that will usually provide the best results.

> Why not extend the current standards that if there are data types that
> their particular application doesn't recognize, they stay around -- just
> ignored.  MacClade does that even with Nexus data (maybe the newest one
> doesn't); but if I save my file from within MacClade, if I want to run
> PAUP again, there are commands that I must reinter into the file
> because MacClade has removed them because it didn't understand them.

I believe that a new format is more desirable than blowing up existing
formats beyond their design specifications. I think the latter is the main
problem that I have with the proposals for "New Delta": The discussion and
proposals correctly identify many shortcomings, which I consider very
valuable work.  However, resolving these issue in the context of the
existing DELTA format structures, and especially in close context to the
way the CSIRO DELTA programs currently work, has lead to many solutions
which I consider undesirable.

Gregor
----------------------------------------------------------
Inst. for Plant Virology, Microbiology, and Biosafety
Federal Research Center for Agriculture and Forestry (BBA)
Gregor Hagedorn                 Net: G.Hagedorn at bba.de
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Often wrong but never in doubt!