Different alignment strategies for indels exist: 3′ alignment or "right aligned" in the field of forensics vs 5' alignment or "left aligned" in field of medical studies/genetics.
For some haplogroups (e.g. 8281d-8289d) correct indels are necessary to get the best hit.
Idea: Fix indels to 3' (since Phylotree is designed that way).
Introduce new optional parameter (--applyAlignmentRules) to fix misplaced alignments