pal.alignment
Interfaces 
Alignment
AnnotationAlignment
CharacterAlignment
Classes 
AbstractAlignment
AlignmentUtils
AminoAcidAlignment
BootstrappedAlignment
CodonAlignment
ConcatenatedAlignment
ConcatenatedAnnotatedAlignment
GapBalancedAlignment
Genotype
IndelAlignment
IndelAnnotatedAlignment
JumbledAlignment
MultiLocusAnnotatedAlignment
ReadAlignment
SimpleAlignment
SimpleAnnotatedAlignment
SimpleCharacterAlignment
SitePattern
StrippedAlignment
StrippedAnnotatedAlignment
Exceptions 
AlignmentParseException