Homologene hasn't been updated since 2014 and isn't going to be according to an eMail I received from the NCBI help desk on November 26th, 2018 saying:
I am not aware of a search that would allow you to specifically search for paralogs. The only way to tell would be to look at a cluster. If it contains more than one gene from the same organism, you could perhaps consider these as paralogs. Proceed with caution as the process for Homologene is completely automated with no manual curation. Also, the last build was in 2014:
https://www.ncbi.nlm.nih.gov/homologene/statistics/
There are currently no plans for a new release.
and
Q: Since Homologene is no longer updated and thus perhaps even outdated (?), would you recommend to only use gene_groups/gene_ortholog for new tools?
A: Yes, I do suggest that (personal suggestion- I am not aware of any NCBI-wide guidelines on this topic).
Keep the top-homology code in place for the future but it won't be used right now.
khituras
commented
4 years ago
Homologene hasn't been updated since 2014 and isn't going to be according to an eMail I received from the NCBI help desk on November 26th, 2018 saying:
and
Keep the top-homology code in place for the future but it won't be used right now.