queeems-package	queeems
aboutQueeems	aboutQueeems
basecensus	baseSummary-class
basecensus,baseSummary-method	baseSummary-class
baseFrequency	baseFrequency
baseSummary	baseSummary-class
baseSummary-class	baseSummary-class
BFs	saturateBF-class
BFs,saturateBF-method	saturateBF-class
BFthreshold	saturateBF-class
BFthreshold,saturateBF-method	saturateBF-class
bstringCodons	bstringCodons
bstringCodons,BStringSet-method	bstringCodons
bstringCodons.BStringSet	bstringCodons
citing	citing-class
citing-class	citing-class
CnCs	CnCs
cncsentropy	cncsentropy
cncsframe	cncsframe-class
cncsframe-class	cncsframe-class
codondifferindex	codondifferindex
codonDissimilarity	codonDissimilarity
codonDissimilarity,BStringSet,numeric-method	codonDissimilarity
codonDissimilarity.BStringSet	codonDissimilarity
datatype	baseSummary-class
datatype,baseSummary-method	baseSummary-class
diffNucBinary	diffNucBinary
entropyindex	entropyindex
fubarweights	fubarweights
geneindex	geneindex-class
geneindex-class	geneindex-class
gentropy	geneindex-class
gentropy,geneindex-method	geneindex-class
II.fasta	queeemsExtdata
informula	geneindex-class
informula,geneindex-method	geneindex-class
informula,siteindices-method	siteindices-class
LogL0	saturateBF-class
LogL0,saturateBF-method	saturateBF-class
LogL1	saturateBF-class
LogL1,saturateBF-method	saturateBF-class
mainPi	saturateBF-class
mainPi,saturateBF-method	saturateBF-class
mnomLogl	mnomLogl
molentropy	molentropy
n2cFreqs	n2cFreqs
nonSynonymous	nonSynonymous
nonvaries	cncsframe-class
nonvaries,cncsframe-method	cncsframe-class
nonvaries,geneindex-method	geneindex-class
nonvaries,saturateBF-method	saturateBF-class
nonvaries,siteindices-method	siteindices-class
nORs	cncsframe-class
nORs,cncsframe-method	cncsframe-class
nseqs	baseSummary-class
nseqs,baseSummary-method	baseSummary-class
nsfreqs	cncsframe-class
nsfreqs,cncsframe-method	cncsframe-class
nucbalance	cncsframe-class
nucbalance,cncsframe-method	cncsframe-class
PI.fasta	queeemsExtdata
queeems	queeems
queeemsExtdata	queeemsExtdata
renyiA	geneindex-class
renyiA,geneindex-method	geneindex-class
renyiA,siteindices-method	siteindices-class
RTI.fasta	queeemsExtdata
saturateBF	saturateBF-class
saturateBF-class	saturateBF-class
seqfilter	seqfilter
seqSaturation	seqSaturation
show, citing-method	citing-class
show,baseSummary-method	baseSummary-class
show,cncsframe-method	cncsframe-class
show,geneindex-method	geneindex-class
show,saturateBF-method	saturateBF-class
show,siteindices-method	siteindices-class
si.renyi	entropyindex
si.shannon	entropyindex
sitecount	geneindex-class
sitecount,geneindex-method	geneindex-class
sitecount,saturateBF-method	saturateBF-class
siteindices	siteindices-class
siteindices-class	siteindices-class
sitentropies	siteindices-class
sitentropies,siteindices-method	siteindices-class
softmax	softmax
summary,saturateBF-method	saturateBF-class
summary,siteindices-method	siteindices-class
useSyn	geneindex-class
useSyn,geneindex-method	geneindex-class
VertCOI.fasta	queeemsExtdata
wildtriplets	cncsframe-class
wildtriplets,cncsframe-method	cncsframe-class
