scoup-package	scoup
aaGamma	aaGamma
aaGauss	aaGauss
aaSCupdate	alignsim
aaSCupdate,discrete-method	discrete-class
aaSCupdate,ou-method	ou-class
aaSCupdate.discrete	alignsim
aaSCupdate.ou	alignsim
aInfo	scoup-class
aInfo,scoup-method	scoup-class
alignsim	alignsim
alignsim,discrete,seqParameters-method	discrete-class
alignsim,omega,seqParameters-method	omega-class
alignsim,ou,seqParameters-method	ou-class
alignsim.discrete	alignsim
alignsim.omega	alignsim
alignsim.ou	alignsim
aminoSC-class	aminoSC-class
asymMean	ou-class
asymMean,ou-method	ou-class
asymVar	ou-class
asymVar,ou-method	ou-class
biTree	biTree
branchL	seqParameters-class
branchL,seqParameters-method	seqParameters-class
codonCoeffs	codonCoeffs
codonFreq	codonFreq
codonvalues-class	codonvalues-class
coeffs	aminoSC-class
coeffs,aminoSC-method	aminoSC-class
coeffs,codonvalues-method	codonvalues-class
cseq	scoup-class
cseq,scoup-method	scoup-class
details	seqParameters-class
details,seqParameters-method	seqParameters-class
discrete-class	discrete-class
discreteInput	discreteInput
dNdS	scoup-class
dNdS,scoup-method	scoup-class
dndsCalculator	dndsCalculator
effpop	alignsim
effpop,discrete-method	discrete-class
effpop,hbParameters-method	hbParameters-class
effpop,omega-method	omega-class
fixMatrix	fixMatrix
freqs	codonvalues-class
freqs,codonvalues-method	codonvalues-class
hbInput	hbInput
hbParameters-class	hbParameters-class
lscape	alignsim
lscape,discrete-method	discrete-class
lscape,omega-method	omega-class
nodes	seqParameters-class
nodes,seqParameters-method	seqParameters-class
nsynVar	alignsim
nsynVar,aminoSC-method	aminoSC-class
nsynVar,hbParameters-method	hbParameters-class
nsynVar,omega-method	omega-class
omega-class	omega-class
ou-class	ou-class
ouEvolve	ouEvolve
ouInput	ouInput
phylogeny	seqParameters-class
phylogeny,seqParameters-method	seqParameters-class
reversion	ou-class
reversion,ou-method	ou-class
sampler	alignsim
sampler,discrete-method	discrete-class
sampler,hbParameters-method	hbParameters-class
sampler,omega-method	omega-class
scoup	scoup
scoup-class	scoup-class
seqCOL	scoup-class
seqCOL,scoup-method	scoup-class
seqDetails	seqDetails
seqParameters-class	seqParameters-class
seqs	scoup-class
seqs,scoup-method	scoup-class
seqWriter	seqWriter
show,aminoSC-method	aminoSC-class
show,codonvalues-method	codonvalues-class
show,discrete-method	discrete-class
show,hbParameters-method	hbParameters-class
show,omega-method	omega-class
show,ou-method	ou-class
show,scoup-method	scoup-class
show,seqParameters-method	seqParameters-class
sites	seqParameters-class
sites,seqParameters-method	seqParameters-class
sitesim	alignsim
sitesim,discrete,numeric-method	discrete-class
sitesim,omega,numeric-method	omega-class
sitesim,ou,numeric-method	ou-class
sitesim.discrete	alignsim
sitesim.omega	alignsim
sitesim.ou	alignsim
subsMatrix	subsMatrix
synVar	aminoSC-class
synVar,aminoSC-method	aminoSC-class
taxa	seqParameters-class
taxa,seqParameters-method	seqParameters-class
tree	biTree
vNvS	alignsim
vNvS,hbParameters-method	hbParameters-class
vNvS,omega-method	omega-class
wInput	wInput
