/usr/share/hyphy/TemplateBatchFiles/SeqAlignmentCodon.bf is in hyphy-common 2.2.7+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 | LoadFunctionLibrary ("SeqAlignmentCodonShared");
checkReferenceSequenceForStopCodons = 1;
doCodonAlignment = 1;
LoadFunctionLibrary ("SeqAlignmentNucShared");
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