I was looking for some Maker-related stuff (not important what) and I realised that there was a new release in April for Maker 2 and Maker 3 was not in beta anymore.
We have been using Maker 2.31.9 in our cluster for a few years now and while the new (2.31.11) includes the most recent change (maker_functional_fasta and maker_functional_gff handle newer UniProt/Swiss-Prot format. Also fix for newer genemark command line structure) I can't find what changed in 2.31.10 nor a general changelog.
By the way, do you know when (version) the genemark command line structure changed? What about the Uniprot format?
Also, is there any fundamental difference aside of the integration of EVM in Maker3 vs Maker2? I found this entry from 2 years ago and wanted to check if this is still the case.