indexGroups.Rd
Group trimmed sequences into aligning groups
indexGroups(blast, fasta, mode = "any", aln.size)
BLAST alignment table to process.
Epitope sequence AAStringset object to process.
Grouping method. "any" creates a smaller number of groups, with individual groups tending to have more members, such that in each group, each member must align with at least 1 "any" of the other members. "all" creates a larger number of groups, with individual groups tending to have fewer members, wuch taht in each group, each member must align with "all" other members.
Minimum length of alignment to consider from BLASTp alignments of 'data'.