Addition Description
Currently, the q2-alignment plugin exposes only a limited set of MAFFT parameters (e.g., --n_threads, --parttree, and --large), but does not provide access to important alignment strategy controls that affect accuracy and runtime trade-offs.
MAFFT provides multiple alignment algorithms (e.g. FFT-NS-2, FFT-NS-i, L-INS-i, G-INS-i, E-INS-i) which are chosen via flags like --localpair, --globalpair, --genafpair, --maxiterate, --nofft, and --retree.
At the moment, users cannot select among these within QIIME 2. Moreover, MAFFT may automatically select the most appropriate algorithm (amongst FFT-NS-1, FFT-NS-2, FFT-NS-i, or L-INS-i) based on input data size via the --auto flag, but this parameter is also not exposed.
Current Behavior
At the moment, the flags --auto, --localpair, --globalpair, --genafpair, --maxiterate, --nofft, and --retree are not exposed to the user.
Proposed Behavior
Expose the parameters listed above so that the user has more granular control over the alignment strategy used. This is especially important when aligning smaller datasets (~200 sequences and less), where more slower but more accurate strategies would be appropriate but are currently not available.
Addition Description
Currently, the q2-alignment plugin exposes only a limited set of MAFFT parameters (e.g.,
--n_threads,--parttree, and--large), but does not provide access to important alignment strategy controls that affect accuracy and runtime trade-offs.MAFFT provides multiple alignment algorithms (e.g. FFT-NS-2, FFT-NS-i, L-INS-i, G-INS-i, E-INS-i) which are chosen via flags like
--localpair,--globalpair,--genafpair,--maxiterate,--nofft, and--retree.At the moment, users cannot select among these within QIIME 2. Moreover, MAFFT may automatically select the most appropriate algorithm (amongst FFT-NS-1, FFT-NS-2, FFT-NS-i, or L-INS-i) based on input data size via the
--autoflag, but this parameter is also not exposed.Current Behavior
At the moment, the flags
--auto,--localpair,--globalpair,--genafpair,--maxiterate,--nofft, and--retreeare not exposed to the user.Proposed Behavior
Expose the parameters listed above so that the user has more granular control over the alignment strategy used. This is especially important when aligning smaller datasets (~200 sequences and less), where more slower but more accurate strategies would be appropriate but are currently not available.