[Taxacom] Molecular data and synapomorphies

Karl Magnacca kmagnacca at wesleyan.edu
Wed Dec 3 08:49:32 CST 2008

On Wed, December 3, 2008 6:56 am, Alan DAvid Forrest wrote:
> FASTA format, to me, was near universal - therefore it is good to
> discover that this is not the case.

It is; it's simply a way of attaching names to sequences in a plain text
file.  Not every program can directly read FASTA files, but the
information can be extracted from any one, which is as universal as you
can get (although I agree that the alignment issue is a problem).  Even
for large multi-sequence datasets, a few steps with find-and-replace in
a word processor can usually convert it to another format.

> I find NEXUS over complex and also have to resort to online
> conversion software, some of which is not very good.

Lines separated by semicolons and begin/end around blocks is too
complex???  Seriously, Nexus is about as simple as you can get.  What on
earth are you expecting to find?

Karl Magnacca
Postdoctoral Researcher
Department of Zoology
Trinity College, Dublin 2

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