Third Party Tools

Members of the user community produce software to assist in the preparation and submission of files to ENA. Some go on to make these more widely available to other users.

The following are tools which are openly available. Please note that we are not responsible for the creation or maintenance of these tools and if you have queries about their use you should contact the creators directly. While we had no hand in their production and have not thoroughly reviewed them, we have heard from users of them that they have been valuable.


A creation of staff at NBI Sweden, this tool can be used to convert an assembly in FASTA format along with associated annotation in GFF3 format into the EMBL flat file format which is the required format for submitting annotated assemblies to us. More information available in their paper:

Artemis Comparison Tool (ACT)

A part of the Artemis Software developed at the Sanger Institute. Among other things, it can output your file in EMBL flat file format.


A tool developed by colleagues at EBI. It can convert between many different formats for various different molecules.


Available for the conversion of annotated DNA multi-sequence alignments in NEXUS format to an EMBL flat file suitable for submission via Webin-CLI. This was developed by Michael Gruenstaeudl and a paper is available with additional detail. DOI: