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OpenTreeOfLife / opentree

Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
http://tree.opentreeoflife.org/
BSD 2-Clause "Simplified" License
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Tree files quality control #725

Open rgazis opened 8 years ago

rgazis commented 8 years ago

Hi

In previous studies I got a red comment, underneath the tree file, warning me of two problems in the tree file:

  1. Show conflicting nodes ---> a) appeared when a taxon or taxa where polyphyletic OR b)when there were multiple terminals with the same name (binomial or genus). For a) I did not do anything since this is the way the author presented the analysis in the publication and reflected the figure, for b) I selected one taxon that represented the group, which seems to fix the problem .
  2. Review ambiguous labels ---> when the tree has branch labels (posterior, bootstrap, or some other labeling), once this is indicated in the properties tab under "Internal node labels represent:", the warning disappears.

HOWEVER

the following study

https://tree.opentreeoflife.org/curator/study/edit/ot_332/?tab=trees

presented both warnings but, when clicking at each warning, both indicate the same problem caused by paraphyletic taxa. This tree has not branch labels so just one warning should appear (#1). Is this a bug? or there are hidden branch labels that are not being shown in the tree visualization screen?

R screen shot 2015-08-27 at 5 07 41 pm

rgazis commented 8 years ago

This is another example in which the tree quality control warns you for ambiguous labels "review ambiguous labels" but there are not labels displayed in the tree - however there are paraphyletic labels (but these should be under "conflicting nodes" right?

https://github.com/opentreeoflife/opentree/issues

rgazis commented 8 years ago

Another example

https://tree.opentreeoflife.org/curator/study/edit/ot_396/?tab=trees