[Biopython-dev] [Biopython - Bug #3407] (New) Handling of bootstrap support values in Bio.Phylo Newick parser

[redmine at redmine.open-bio.org]

Issue #3407 has been reported by Ben Morris.

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Bug #3407: Handling of bootstrap support values in Bio.Phylo Newick parser
https://redmine.open-bio.org/issues/3407

Author: Ben Morris
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


This was reported to me by Arlin Stoltzfus (quote):


"There is a description of Newick here: 

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

and a BNF here: 

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

Note that this allows square-bracketed comments. 

Bootstrap values commonly are represented in 2 ways, one of which is wrong.  The wrong way to represent bootstrap values is to present them as internal node labels.   Labels for internal nodes are given as follows: 

   ((( human: 0.1, chimp:0.1 ) primates: 0.2, (rat:0.1, mouse:0.1) rodents:0.2), cat:0.3 )

where "primates" and "rodents" are internal node labels.  They go between the right paren and the (optional) colon and distance.  If you put numbers in the label position, a graphic renderer may place them on the nodes, which is why some people represent bootstrap values this way. 

However, the preferred way to represent bootstrap values is to make them syntactic comments (enclosed in square brackets) placed after all other node information, i.e., after the optional colon & branch length.   Both examples are shown here: 

((raccoon:19.19959,bear:6.80041)50:0.84600,((sea_lion:11.99700, seal:12.00300)100:7.52973,((monkey:100.85930,cat:47.14069)80:20.59201, weasel:18.87953)75:2.09460)50:3.87382,dog:25.46154);
or
((raccoon:19.19959,bear:6.80041):0.84600[50],((sea_lion:11.99700, seal:12.00300):7.52973[100],((monkey:100.85930,cat:47.14069):20.59201[80], weasel:18.87953):2.09460[75]):3.87382[50],dog:25.46154);

I recommend that you only support the second version, and treat the first version as a case of internal node labels.  

Arlin
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Arlin Stoltzfus (arlin at umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850
tel: 240 314 6208; web: www.molevol.org"


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