When a taxon isn't in the synthetic tree, the reason for that should be provided

[jar398]

See discussion here:
https://groups.google.com/forum/#!topic/opentreeoflife-software/raWZ7hSfUpI

and corresponding treemachine issue here:
OpenTreeOfLife/treemachine#98

As a first step, before the treemachine service is in place, there should be generic static text saying that the taxon is not in the synthetic tree, either because it is determined to be paraphyletic, or because it was omitted for taxonomic reasons (e.g. it was incertae sedis).

[jar398]

Can we as a stopgap just display some static text whenever this happens? Something like the following:

"This taxon was not found in the synthetic tree. Usually this happens for one of the following reasons:

1. The taxon is incompatible with one of the phylogenetic trees that were input to synthesis, i.e. it does not seem to be monophyletic.
2. The taxon was excluded because it did not have a designated location in the taxonomy (incertae sedis)."

Not that this is a beautiful explanation - we can improve on it - but I think it goes to branding and reputation to do something in this situation; we have seen PIs on the project who don't remember this even after having it explained to them.

Then after we get the needed service from treemachine or taxomachine (as the case may be), we can provide some useful information, such as what trees conflict with monophyly, or what taxonomic information is missing (i.e. what the incomplete lineage is).

[jimallman]

Can we as a stopgap just display some static text whenever this happens?

This is working now, including a link to the taxon in our taxonomy browser. OK to close this, or do we still want to offer a fuller explanation on demand?

[jar398]

Working great.