Here is a list of all functions, variables, defines, enums, and typedefs with links to the files they belong to:

- a -

• aachar : genwin.c , genwin.h
• aaflag : genwin.c
• aaindex : genwin.c , genwin.h
• abets : genwin.c
• ABS : karlin.c
• alignment_freeAlignment() : alignments.c
• alignment_unpackSubject() : alignments.h
• alignments_addFinalAlignment() : alignments.h , alignments.c
• alignments_addGappedExtension() : alignments.h , alignments.c
• alignments_addGoodAlignment() : alignments.c
• alignments_addUngappedExtension() : alignments.c , alignments.h
• alignments_addUngappedExtensionAtEnd() : alignments.c
• alignments_alignments : alignments.h
• alignments_checkForJoin() : alignments.c
• alignments_compareAlignmentDescriptionLocations() : alignments.c
• alignments_compareCodeword() : index.c
• alignments_compareFinalAlignments() : alignments.c
• alignments_compareQueryPosition() : index.c
• alignments_contains() : alignments.c
• alignments_createNew() : alignments.c , alignments.h
• alignments_currentAlignment : alignments.h
• alignments_expandCluster() : alignments.c
• alignments_finalAlignments : alignments.h
• alignments_finalAlignmentsSorted : alignments.c
• alignments_findFinalAlignments() : alignments.h , alignments.c
• alignments_findGoodAlignments() : alignments.c , alignments.h
• alignments_findTopFinalAlignments() : alignments.c
• alignments_free() : alignments.h , alignments.c
• alignments_getFinalAlignmentDescriptions() : alignments.c , alignments.h
• alignments_getTracebacks() : alignments.c , alignments.h
• alignments_goodAlignments : alignments.h
• alignments_initialize() : alignments.c , alignments.h
• alignments_isFinalAlignment() : alignments.h , alignments.c
• alignments_loadSubjectsIntoMemory() : alignments.c , alignments.h
• alignments_moveGoodToFinal() : alignments.c
• alignments_numClusters : alignments.c , alignments.h
• alignments_numVolumes : alignments.c
• alignments_performScoring() : alignments.h
• alignments_printFinalAlignments() : alignments.c
• alignments_printGoodAlignments() : alignments.c
• alignments_pruneOverlappingExtensions() : alignments.c
• alignments_pruneRegion() : alignments.c
• alignments_regularGappedAlignment() : alignments.c
• alignments_removeGappedExtension() : alignments.c
• alignments_selectRegion() : alignments.c
• alignments_sortFinalAlignments() : alignments.c , alignments.h
• alignments_sortGoodAlignments() : alignments.c
• alignments_unpruneRegion() : alignments.c
• alignments_volumeAlignments : alignments.c
• appendseg() : seg.c

---