One of the default tools to generate EMBL flat files from NEXUS-formatted multiple sequence alignments is the "old workhorse" Sequin. I also understand that the genome browser Artemis has a similar functionality, and Artemis is the recommended method for the conversion nex2embl. Neither tool has commandline abilities, however.
The Bio.SeqIO interface in BioPython includes some excellent parsers to read and write the NEXUS multiple alignment and the EMBL flat file formats, respectively. Hence, it provides the functionality necessary to convert NEXUS-formatted DNA sequence alignments into a multi-sequence EMBL flat file.
A similar functionality, I would assume, is provided by BioPerl (but I am not a Perl programmer, so this is just speculation).
Are there any commandline alternatives besides the Python or Perl interpreters to perform the conversion from NEXUS to the EMBL flat file with the intent of generating a submission-ready flat file? For so common a task I would have expected to find more bioinformatic tools, especially on Github.