Wiki source code of Data formats for trees

Last modified by 14zunde on 2024/02/13 07:41
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1 There are a number of [[data formats>>doc:stemmatology.Data formats.WebHome]] for representing phylogenetic or other kinds of [[trees>>doc:stemmatology.Tree.WebHome]]. Perhaps the most common one, which shall be discussed here exemplarily, is Newick. It uses brackets in quite an intuitive way. R(% style="line-height: 1.4285715;" %)epresentation on various levels of detail are possible. For example, the two strings
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5 {{{    (A, (B, (C, D)));    (A:1.0,(B:0.6,(C:0.2,D:0.1):0.6):0.2);}}}
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7 encode the same [[bifurcating>>doc:stemmatology.Bifid binary bifurcating bipartite.WebHome]] tree topology with four labelled leaf [[nodes>>doc:stemmatology.Node (vertex).WebHome]], respectively with and without [[edge>>doc:stemmatology.Edge.WebHome]] lengths. The resulting trees are shown in Fig. 1.
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9 ==== Illustration ====
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13 (% style="margin-left: 90.0px;" %)
14 [[image:attach:exABCD1.png]][[image:attach:exABCD2.png]]
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16 Fig. 1: Left: A tree without edge lengths. Right: A tree with edges drawn proportional to their lengths. The edge lengths are also shown as numbers. (The figures were drawn using the program FigTree.)
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20 If the tree is [[unrooted>>doc:stemmatology.Root.WebHome]], an arbitrary node is chosen to be used first. Any node may be specified as root in the tree in this format. The format uses the file extension .nwk. It is used for instance in [[Phylip>>doc:stemmatology.PHYLIP.WebHome]], [[doc:stemmatology.MrBayes.WebHome]] and [[doc:stemmatology.PAUP.WebHome]]*.
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24 [[TR>>doc:stemmatology.Parvum lexicon stemmatologicum.Contributors.WebHome]], [[PR>>doc:stemmatology.Parvum lexicon stemmatologicum.Contributors.WebHome]]
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