ETE3: error while parsing Newick tree
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Entering edit mode
2.9 years ago

Any idea why ETE Toolkit (ete3) throws an error while parsing the following Newick tree:

((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N));

from ete3 import Tree
s = '((((A,B),C),(((D,E),F),(((((G,H),I),J),K),L)))(M,N));'
t = Tree(s)

The error message:

ete3.parser.newick.NewickError: Broken newick structure at: G,H),I),J),K),L)))
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

I also tried loading the tree with all the format flag (and values from 0 to 9).

ete3 newick tree ete • 1.4k views
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3
Entering edit mode
2.9 years ago
Mensur Dlakic ★ 20k

You need comma between L))) and (M,N).

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