Talk:Newick format
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Leaf Names
[edit]Is it mandatory for the leaves to have names in Newick format? The example list includes a tree with no node names at all, but this seems to violate the grammar given below it. (Unless the terminal "name" can also be an empty string.) 2001:DF0:0:2006:1A03:73FF:FEDC:2A06 (talk) —Preceding undated comment added 04:35, 18 October 2012 (UTC)
- Yes, the terminal Name can also be empty.—Quantling (talk | contribs) 21:21, 21 October 2012 (UTC)
Branch Length Units
[edit]The branch lengths supplied in Newick format, what are their units? Vegar Ottesen 14:23, 19 November 2013 (UTC)
- It is not specified. I have seen years (or megayears, etc.). I have seen the number of mutations a position of junk DNA will have undergone on average. Perhaps there are other possibilities. —Quantling (talk | contribs) 17:09, 9 April 2025 (UTC)
dnd extension
[edit]I'm wondering if anyone can make a statement on the main page on why it is so common to have a DND extension for Newick trees.--158.111.4.53 (talk) 15:01, 27 June 2014 (UTC)
Extended Newick
[edit]The phylogenetic networks page mentions that there is an extended version of the Newick format for phylogenetic networks. Is it reasonable to add that on this page, or should it get its own page? RemJanssen (talk) 15:29, 18 August 2018 (UTC)
Branch Length on leaf nodes
[edit]If I'm reading the grammar correctly, it allows length on Internal nodes but not on Leaf notes. But this seems incorrect, since leaf nodes can have lengths, and do in several of the examples (e.g. "(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);").
Instead of 'Leaf → Name', should it be 'Leaf → Name Length'? David Ebbo (talk) 21:39, 12 February 2023 (UTC)
- The grammar in http://scikit-bio.org/docs/0.2.2/generated/skbio.io.newick.html appears more correct and does not have this issue. David Ebbo (talk) 21:45, 12 February 2023 (UTC)
- Perhaps the tokens should be renamed to make this clearer? An expression such as "A:0.1" is a branch (that has a length 0.1 and leads to a node that is a leaf named "A"). —Quantling (talk | contribs) 16:28, 13 February 2023 (UTC)