Plugins

Perform de novo multiple sequence alignment using MAFFT.

Add new sequences to an existing alignment with MAFFT.

Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).

Trim an existing alignment based on provided primers or specific, pre-defined positions. Primers take precedence over the positions,i.e. if both are provided, positions will be ignored.When using primers in combination with a DNA alignment, a new alignment will be generated to locate primer positions. Subsequently, start (5'-most) and end (3'-most) position from fwd and rev primer located within the new alignment is identified and used for slicing the original alignment. The retention of alignment positions that span the primer locations can be toggled. WARNING: finding alignment positions via primer search can be inefficient for very large alignments and is only recommended for small alignments. For large alignments providing specific alignment positions is ideal.

Annotate MAGs or contigs with antimicrobial resistance genes with AMRFinderPlus. Check https://github.com/ncbi/amr/wiki for documentation.

Takes a collection of GenomeData[AMRFinderPlusAnnotations] and collates them into a single artifact.

Create a gene/class/subclass per contig frequency table from AMRFinderPlus annotations.

Download the latest version of the AMRFinderPlus database.