Prank appears to remove terminal stop codons. This is done by VESPA later on in the pipeline to format the alignments for CodeML, however, the removal in Prank is premature and results in the input alignments not having the same number of amino acids. Therefore metAl compare does not work. Muscle and Mafft alignments work, when the headers are the same, generally in a format of SpeciesCommonName_EnsemblID|TranscriptID
Prank appears to remove terminal stop codons. This is done by VESPA later on in the pipeline to format the alignments for CodeML, however, the removal in Prank is premature and results in the input alignments not having the same number of amino acids. Therefore metAl compare does not work. Muscle and Mafft alignments work, when the headers are the same, generally in a format of SpeciesCommonName_EnsemblID|TranscriptID