Addition Description
Add the ability for q2-alignment to accept protein sequences as input for alignment.
Current Behavior
Currently, q2-alignment only accepts nucleotide sequences (DNA/RNA) as input for alignment. Attempting to provide amino acid sequences results in an error.
Proposed Behavior
Enable q2-alignment to accept FeatureData[ProteinSequence] as an input and output FeatureData[AlignedProteinSequence]. ProteinFASTAFormat and AlignedProteinFASTAFormat may be used as the directory format for each respective type.
MAFFT already provide support for both nucleotide and protein alignments via the --nuc and --amino flags, but the sequence type can also be detected automatically (default behavior).
Comments
This feature would be particularly useful for constructing phylogenies from conserved protein domains.
Addition Description
Add the ability for q2-alignment to accept protein sequences as input for alignment.
Current Behavior
Currently, q2-alignment only accepts nucleotide sequences (DNA/RNA) as input for alignment. Attempting to provide amino acid sequences results in an error.
Proposed Behavior
Enable q2-alignment to accept
FeatureData[ProteinSequence]as an input and outputFeatureData[AlignedProteinSequence].ProteinFASTAFormatandAlignedProteinFASTAFormatmay be used as the directory format for each respective type.MAFFT already provide support for both nucleotide and protein alignments via the
--nucand--aminoflags, but the sequence type can also be detected automatically (default behavior).Comments
This feature would be particularly useful for constructing phylogenies from conserved protein domains.