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LegumeFederation / Interface-and-Usability

Repo for tracking issues on LegFed interface and usability
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gene family trees expanded to include all legume species #5

Open amcooksey opened 6 years ago

amcooksey commented 6 years ago

This may have already been addressed--Steven was re-calculating gene families recently. If you have a gene from lupine you won't find it in the family tree display despite linking out from the appropriate gene family name on the lupine gene page. There is also a link to take you to the high-lighted gene in the tree but it doesn't you anywhere because the gene isn't there.

adf-ncgr commented 6 years ago

Hi- although @cann0010 has indeed recalculated trees with the current set of species, this issue will not be completely solved by that. For example, even with respect to legumeinfo genomes only cicar.CDCFrontier (kabuli chickpea) and not cicar.ICC4958 (desi chickpea) will be in the trees, and the same will be true of many federated species (e.g. wild chickpea "cicre", or the medicago hapmap genomes). What I'd like to do is provide a way to have the missing genes added (at user request) through the power of lorax; most of the pieces of this puzzle are in place already, it probably just needs a little focus and coordination to make it happen. This will have some possible implications for connectivity from the resulting tree back to GCV (see legumeinfo/lis_context_viewer#94, specifically the comment that links back to this one...)