| aligned_coords_s | Store a pair of aligned positions and the characters |
| AlignedCoordSeqIComparator | |
| AluRecord | |
| AnalRowComp | |
| BbSeqComp | |
| BbSorter | |
| CompactMatchRecord | |
| CompactUngappedMatchRecord | An ungapped alignment that also stores a match record |
| GappedMatchRecord | The gapped match record class |
| IntervalCompare | |
| IntervalMap | |
| IntervalSeqManipulator | |
| IsNullPtr< T > | |
| livComp | |
| LocComp | |
| MatchLink | Stores a link between a subset and a superset match |
| MatchRecord | |
| MatchSortEntryCompare | |
| MauveOption | |
| MLDeleter | |
| NeighborhoodGroupCompare | |
| NeighborhoodGroupComponentCompare | |
| NeighborhoodListComparator | Used to sort the neighborhood list using std::sort |
| NeighborhoodListEntry | This class stores a single entry in the neighborhood list |
| NllBuffers | Temporary buffers that get used every time a neighborhood list lookup is performed |
| OptionList | |
| PairFirstComparator< PairType > | |
| ProcrastinationQueue | A class to prioritize match records for extension based on their multiplicity |
| ProcrastinationQueue::MultiplicityHeapCompare | Defines a multiplicity heap ordering |
| SeedMatchEnumerator | Turns every seed match into a full match without extension |
| ShorterThan | |
| TaxonNamePairComparator | |
| TheRealMemHash | |
| ToUPPER | |
| TreeIntervalMap | |
| UngappedMatchRecord | An ungapped alignment that also stores a match record |
| UniqueMatchFinder | Finds all pairwise matches with unique seeds among a group of sequences |
| VectorIntervalMap |
1.3.6