[Biojava-l] A question about NexusFile and NewickTreeString

[Hilmar Lapp]

Tiago - the authoritative page on Newick format is here:

http://evolution.genetics.washington.edu/phylip/newicktree.html

NHX (New Hampshire Extended) is here:

http://www.phylosoft.org/NHX/

	-hilmar

On Dec 18, 2009, at 7:23 AM, Tiago Antão wrote:

> Hi,
>
> 2009/12/15 Hilmar Lapp <hlapp at drycafe.net>:
>> Actually no. Ancestor1 is the node label of the ancestor node of A,  
>> C, and
>> E. Node labels follow after a parenthesis without a comma.
>
>
> I think I've found the cause for this mistake: I was following
> http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_NEXUS_Format
> which happens not to discuss newick trees in sufficient detail. I
> should have used a more detailed spec.
> I've found this:
> http://en.wikipedia.org/wiki/Newick_format
> Question:
> I am assuming that the name string is a string in the usual sense, ie,
> something starting with an alpha (not numeric) and ending in the first
> whitespace.
> Given your experience with the format (and considering that sometimes
> de facto implementations are somewhat liberal), do you think this
> notion of string is good enough?
>
> If so, the change seems trivial and should be ready today.
>
> Tiago
> -- 
> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci

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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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