alakazam-package	alakazam
ABBREV_AA	ABBREV_AA
AbundanceCurve	AbundanceCurve-class
AbundanceCurve-class	AbundanceCurve-class
AbundanceCurve-method	AbundanceCurve-class
alakazam	alakazam
aliphatic	aliphatic
alphaDiversity	alphaDiversity
aminoAcidProperties	aminoAcidProperties
baseTheme	baseTheme
buildPhylipLineage	buildPhylipLineage
bulk	bulk
calcCoverage	calcCoverage
calcDiversity	calcDiversity
ChangeoClone	ChangeoClone-class
ChangeoClone-class	ChangeoClone-class
charge	charge
checkColumns	checkColumns
collapseDuplicates	collapseDuplicates
combineIgphyml	combineIgphyml
countClones	countClones
countGenes	countGenes
countPatterns	countPatterns
cpuCount	cpuCount
DEFAULT_COLORS	DEFAULT_COLORS
DiversityCurve	DiversityCurve-class
DiversityCurve-class	DiversityCurve-class
DiversityCurve-method	DiversityCurve-class
DNA_COLORS	DEFAULT_COLORS
EdgeTest	EdgeTest-class
EdgeTest-class	EdgeTest-class
EdgeTest-method	EdgeTest-class
estimateAbundance	estimateAbundance
ExampleDb	ExampleDb
ExampleTrees	ExampleTrees
extractVRegion	extractVRegion
getAAMatrix	getAAMatrix
getAllele	getSegment
getDNAMatrix	getDNAMatrix
getFamily	getSegment
getGene	getSegment
getMRCA	getMRCA
getPathLengths	getPathLengths
getSegment	getSegment
graphToPhylo	graphToPhylo
gravy	gravy
gridPlot	gridPlot
groupGenes	groupGenes
IG_COLORS	DEFAULT_COLORS
IMGT_REGIONS	IMGT_REGIONS
isValidAASeq	isValidAASeq
IUPAC_AA	IUPAC_CODES
IUPAC_CODES	IUPAC_CODES
IUPAC_DNA	IUPAC_CODES
makeChangeoClone	makeChangeoClone
makeTempDir	makeTempDir
maskSeqEnds	maskSeqEnds
maskSeqGaps	maskSeqGaps
MRCATest	MRCATest-class
MRCATest-class	MRCATest-class
MRCATest-method	MRCATest-class
nonsquareDist	nonsquareDist
padSeqEnds	padSeqEnds
pairwiseDist	pairwiseDist
pairwiseEqual	pairwiseEqual
permuteLabels	permuteLabels
phyloToGraph	phyloToGraph
plot,AbundanceCurve,missing-method	AbundanceCurve-class
plot,DiversityCurve,missing-method	DiversityCurve-class
plot,DiversityCurve,numeric-method	DiversityCurve-class
plot,EdgeTest,missing-method	EdgeTest-class
plot,MRCATest,missing-method	MRCATest-class
plotAbundanceCurve	plotAbundanceCurve
plotDiversityCurve	plotDiversityCurve
plotDiversityTest	plotDiversityTest
plotEdgeTest	plotEdgeTest
plotMRCATest	plotMRCATest
plotSubtrees	plotSubtrees
polar	polar
print,AbundanceCurve-method	AbundanceCurve-class
print,DiversityCurve-method	DiversityCurve-class
print,EdgeTest-method	EdgeTest-class
print,MRCATest-method	MRCATest-class
progressBar	progressBar
rarefyDiversity	rarefyDiversity
readChangeoDb	readChangeoDb
readIgphyml	readIgphyml
seqDist	seqDist
seqEqual	seqEqual
sortGenes	sortGenes
stoufferMeta	stoufferMeta
summarizeSubtrees	summarizeSubtrees
tableEdges	tableEdges
testDiversity	testDiversity
testEdges	testEdges
testMRCA	testMRCA
translateDNA	translateDNA
translateStrings	translateStrings
TR_COLORS	DEFAULT_COLORS
writeChangeoDb	writeChangeoDb
