Purpose: This tool is designed to help determine if a newly defined clade of related sequences should most appropriately be considered a new subtype, a new sub-subtype, or part of a previously defined subtype.
Details: SUDI should be used in conjunction with other tools that will identify recombination and phylogenetic relationships. The purpose of this tool is to determine tree-based genetic distances for a new cluster relative to known subtypes, and then to compare these distances to typical distances found among pre-existing subtypes.
To use this tool, you can either enter a sequence alignment and create a neighbor joining tree to serve as the basis for the genetic distances, or you can enter your own tree in the form of a PHYLIP outfile. The format of the input sequence names is critical.
Please read the SUDI Explanation carefully before using this program.