If you would like to convert a file from one format to another, you can do so using ConKit’s provided script, which is called conkit-convert.
$> conkit-convert toxd/toxd.a3m a3m toxd/toxd.mfa fasta
The call above converts the toxd.a3m file, which is in a3m format, to the toxd.mfa file in fasta format.
You can convert these files to many different other formats, for a full list check out the Table of available file formats.