Re: [CDAO-discuss] Need a concept for the "pseudo-root" of an unrooted tree

[Arlin S. <ar...@um...>]

I think "render anchor" captures the needed concept more clearly.  

Another option is to allow node A is_root_of tree B  but assign it 0 confidence.  

It is important to note that the issue Ben raises has existed for decades.    It would be great to solve this problem in a way that is consistent with current practices and expectations, but I'm not sure exactly what they are.  My impression is that systematists tend to be more careful about designating outgroups, whereas molecular evolutionists and others produce unrooted trees and depict them as rooted trees without thinking about it too much (most molecular phylogenies are inferred using time-symmetric models, so they are not rooted). Some software uses a 3-way basal polytomy as a cryptic signal that the tree is unrooted.  Alas, this cryptically unrooted tree is indistinguishable from a rooted tree with a 3-way basal polytomy.  Other software may use [&U] and [&R].   

Arlin

On Jun 30, 2013, at 9:58 PM, Matt Yoder wrote:

> It sounds like this concept is specifically (only?) used for
> rendering?  How about making it specific and calling it a "render
> anchor" or some such?
> 
> Cheers,
> Matt
> 
> On Sat, Jun 29, 2013 at 5:03 PM, Ben Morris <be...@be...> wrote:
>> A few of us discussed this briefly at iEvoBio; it would be great to
>> have a concept similar to "has_Root", but for unrooted trees. Some
>> tree formats, such as Newick, represent rooted and unrooted trees
>> identically - an unrooted tree has a "pseudo-root" and is represented
>> the same way as a rooted tree. The position of this pseudo-root is
>> completely arbitrary. If a Newick tree is converted to CDAO and then
>> back to Newick, the resulting tree may appear to be "rooted"
>> differently than the original. While this is technically fine (since
>> it's unrooted, it shouldn't matter where the "pseudo-root" is placed),
>> it may be confusing or irritating to users. Having a property
>> cdao:has_PseudoRoot would ensure that the tree could be retrieved from
>> a triple store and converted back to a Newick tree without changing
>> the position of the pseudo-root - so users would get back a tree that
>> they could easily verify was identical to what they started with.
>> 
>> Currently I'm using has_Root for unrooted trees; this is certainly
>> incorrect, as the pseudo-root is not a root. It's important to
>> distinguish between a true root and what's merely a starting point for
>> convenience but has no real meaning.
>> 
>> 
>> Ben Morris
>> PhD student, Ecology/Evolutionary Biology
>> University of North Carolina, Chapel Hill, NC
>> Mail: be...@be... | Twitter: @bendmorris
>> Web: www.bendmorris.com
>> 
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Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
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