Returns Strings to avoid lifetime issues
Coordinate transforming - from align to chr
Basic stats on alignments
Coordinate transforming - from chr to align
Returns unpolarized substitutions
Get the next Axt block out of the input.
Get the next FasBlock out of the input.
Get the next MafBlock out of the input.
Divergence (D) between two sequences
Polarize substitutions
Records complex ingroup indels (ingroup-outgroup complex indels are not identified here)
Trims head and tail indels.
Returns a Vecter of Tuple(head, tail) corresponding to the bases deleted from each sequence
Trims outgroup-only regions
Trims pure dash regions