Index

A
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.Nucleotide
6 (Data Constructor)	ELynx.Data.Character.NucleotideI
7 (Data Constructor)	ELynx.Data.Character.NucleotideX
all	ELynx.Data.Alphabet.Alphabet
Allele	ELynx.Data.Character.BoundaryMutation
AlleleCount	ELynx.Data.Character.BoundaryMutation
Alphabet	ELynx.Data.Alphabet.Alphabet
alphabet
1 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.Data.Sequence.Sequence
alphabetNameVerbose	ELynx.Data.Alphabet.Alphabet
AlphabetSpec
1 (Type/Class)	ELynx.Data.Alphabet.Alphabet
2 (Data Constructor)	ELynx.Data.Alphabet.Alphabet
alphabetSpec	ELynx.Data.Alphabet.Alphabet
AminoAcid	ELynx.Data.Character.AminoAcid
AminoAcidI	ELynx.Data.Character.AminoAcidI
AminoAcidS	ELynx.Data.Character.AminoAcidS
AminoAcidX	ELynx.Data.Character.AminoAcidX
appendName
1 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.Data.MarkovProcess.MixtureModel
B
1 (Data Constructor)	ELynx.Data.Character.AminoAcidI
2 (Data Constructor)	ELynx.Data.Character.NucleotideI
Bnd	ELynx.Data.Character.BoundaryMutation
bndA	ELynx.Data.Character.BoundaryMutation
bndN	ELynx.Data.Character.BoundaryMutation
C
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.Nucleotide
6 (Data Constructor)	ELynx.Data.Character.NucleotideI
7 (Data Constructor)	ELynx.Data.Character.NucleotideX
c10StatDists	ELynx.Data.MarkovProcess.CXXModelsData
c10Weights	ELynx.Data.MarkovProcess.CXXModelsData
c20StatDists	ELynx.Data.MarkovProcess.CXXModelsData
c20Weights	ELynx.Data.MarkovProcess.CXXModelsData
c30StatDists	ELynx.Data.MarkovProcess.CXXModelsData
c30Weights	ELynx.Data.MarkovProcess.CXXModelsData
c40StatDists	ELynx.Data.MarkovProcess.CXXModelsData
c40Weights	ELynx.Data.MarkovProcess.CXXModelsData
c50StatDists	ELynx.Data.MarkovProcess.CXXModelsData
c50Weights	ELynx.Data.MarkovProcess.CXXModelsData
c60StatDists	ELynx.Data.MarkovProcess.CXXModelsData
c60Weights	ELynx.Data.MarkovProcess.CXXModelsData
Character
1 (Type/Class)	ELynx.Data.Character.Character
2 (Type/Class)	ELynx.Data.Alphabet.Character
CharacterI	ELynx.Data.Character.Character
characters	ELynx.Data.Sequence.Sequence
CharacterX	ELynx.Data.Character.Character
Chrom	ELynx.Export.Sequence.CountsFile
Codon
1 (Type/Class)	ELynx.Data.Character.Codon
2 (Data Constructor)	ELynx.Data.Character.Codon
Component
1 (Type/Class)	ELynx.Data.MarkovProcess.MixtureModel
2 (Data Constructor)	ELynx.Data.MarkovProcess.MixtureModel
concatenate
1 (Function)	ELynx.Data.MarkovProcess.MixtureModel
2 (Function)	ELynx.Data.Sequence.Sequence
concatenateSeqs	ELynx.Data.Sequence.Sequence
convert	ELynx.Data.Character.Character
countGaps	ELynx.Data.Sequence.MultiSequenceAlignment
countIUPACChars	ELynx.Data.Sequence.MultiSequenceAlignment
countUnknowns	ELynx.Data.Sequence.MultiSequenceAlignment
cxx	ELynx.Data.MarkovProcess.CXXModels
D
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
DataOneSite	ELynx.Export.Sequence.CountsFile
defFieldWidth	ELynx.Data.Sequence.Defaults
defSequenceListSummaryNumber	ELynx.Data.Sequence.Defaults
defSequenceNameWidth	ELynx.Data.Sequence.Defaults
defSequenceSummaryLength	ELynx.Data.Sequence.Defaults
DNA	ELynx.Data.Alphabet.Alphabet
DNAI	ELynx.Data.Alphabet.Alphabet
DNAX	ELynx.Data.Alphabet.Alphabet
E
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
EDMComponent	ELynx.Data.MarkovProcess.EDMModel, ELynx.Import.MarkovProcess.EDMModelPhylobayes
edmModel	ELynx.Data.MarkovProcess.EDMModel
entropy	ELynx.Data.Alphabet.DistributionDiversity
equalLength	ELynx.Data.Sequence.Sequence
ExchangeabilityMatrix	ELynx.Data.MarkovProcess.RateMatrix
exchangeabilityMatrix	ELynx.Data.MarkovProcess.SubstitutionModel
expand	ELynx.Data.MarkovProcess.GammaRateHeterogeneity
F
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
fasta	ELynx.Import.Sequence.Fasta
fastaSequence	ELynx.Import.Sequence.Fasta
filterColumnsNoGaps	ELynx.Data.Sequence.MultiSequenceAlignment
filterColumnsOnlyStd	ELynx.Data.Sequence.MultiSequenceAlignment
filterColumnsStd	ELynx.Data.Sequence.MultiSequenceAlignment
filterLongerThan	ELynx.Data.Sequence.Sequence
filterShorterThan	ELynx.Data.Sequence.Sequence
frequencyCharacters	ELynx.Data.Alphabet.DistributionDiversity
FrequencyData	ELynx.Data.Sequence.MultiSequenceAlignment
fromChar
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
fromCharacters	ELynx.Data.Sequence.Sequence
fromCVec	ELynx.Data.Alphabet.Character
fromExchangeabilityMatrix	ELynx.Data.MarkovProcess.RateMatrix
fromIndexWith	ELynx.Data.Character.BoundaryMutation
fromSequenceList	ELynx.Data.Sequence.MultiSequenceAlignment
fromString
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
fromSubstitutionModels	ELynx.Data.MarkovProcess.MixtureModel
fromWord
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
G
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.Nucleotide
6 (Data Constructor)	ELynx.Data.Character.NucleotideI
7 (Data Constructor)	ELynx.Data.Character.NucleotideX
Gap
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.NucleotideI
5 (Data Constructor)	ELynx.Data.Character.NucleotideX
gap
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Alphabet
getAlphabet
1 (Function)	ELynx.Data.MarkovProcess.MixtureModel
2 (Function)	ELynx.Data.MarkovProcess.PhyloModel
getRateMatrix	ELynx.Data.MarkovProcess.SubstitutionModel
getStationaryDistribution	ELynx.Data.MarkovProcess.RateMatrix
getSubstitutionModels	ELynx.Data.MarkovProcess.MixtureModel
getWeights	ELynx.Data.MarkovProcess.MixtureModel
H
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
hky	ELynx.Data.MarkovProcess.Nucleotide
homoplasy	ELynx.Data.Alphabet.DistributionDiversity
I
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
isGap
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Alphabet
isIUPAC
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Alphabet
isMember	ELynx.Data.Alphabet.Alphabet
isStandard	ELynx.Data.Character.Character
isStd	ELynx.Data.Alphabet.Alphabet
isUnknown
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Alphabet
isValid	ELynx.Data.MarkovProcess.MixtureModel
iupac
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Alphabet
J	ELynx.Data.Character.AminoAcidI
jc	ELynx.Data.MarkovProcess.Nucleotide
jump	ELynx.Simulate.MarkovProcess
K
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
kEffEntropy
1 (Function)	ELynx.Data.Alphabet.DistributionDiversity
2 (Function)	ELynx.Data.Sequence.MultiSequenceAlignment
kEffHomoplasy
1 (Function)	ELynx.Data.Alphabet.DistributionDiversity
2 (Function)	ELynx.Data.Sequence.MultiSequenceAlignment
L
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
lengthSequence	ELynx.Data.Sequence.Sequence
lg	ELynx.Data.MarkovProcess.AminoAcid
lgCustom	ELynx.Data.MarkovProcess.AminoAcid
lgCustomUnnormalized	ELynx.Data.MarkovProcess.AminoAcid
longest	ELynx.Data.Sequence.Sequence
M
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
MixtureModel
1 (Type/Class)	ELynx.Data.MarkovProcess.MixtureModel
2 (Data Constructor)	ELynx.Data.MarkovProcess.MixtureModel
3 (Data Constructor)	ELynx.Data.MarkovProcess.PhyloModel
msaConcatenate	ELynx.Data.Sequence.MultiSequenceAlignment
msaJoin	ELynx.Data.Sequence.MultiSequenceAlignment
msaLength	ELynx.Data.Sequence.MultiSequenceAlignment
msaNSequences	ELynx.Data.Sequence.MultiSequenceAlignment
msasConcatenate	ELynx.Data.Sequence.MultiSequenceAlignment
MultiSequenceAlignment
1 (Type/Class)	ELynx.Data.Sequence.MultiSequenceAlignment
2 (Data Constructor)	ELynx.Data.Sequence.MultiSequenceAlignment
N
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
Name	ELynx.Data.MarkovProcess.SubstitutionModel
name
1 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.Data.MarkovProcess.MixtureModel
3 (Function)	ELynx.Data.Sequence.Sequence
neighbors	ELynx.Data.Character.BoundaryMutation
nFixed	ELynx.Data.Character.BoundaryMutation
normalize
1 (Function)	ELynx.Data.MarkovProcess.RateMatrix
2 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
3 (Function)	ELynx.Data.MarkovProcess.MixtureModel
normalizeWith	ELynx.Data.MarkovProcess.RateMatrix
Nucleotide	ELynx.Data.Character.Nucleotide, ELynx.Data.Character.BoundaryMutation
NucleotideI	ELynx.Data.Character.NucleotideI
NucleotideX	ELynx.Data.Character.NucleotideX
P
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
Params	ELynx.Data.MarkovProcess.SubstitutionModel
Parser	ELynx.Import.MarkovProcess.EDMModelPhylobayes
phylobayes	ELynx.Import.MarkovProcess.EDMModelPhylobayes
PhyloModel	ELynx.Data.MarkovProcess.PhyloModel
Ply	ELynx.Data.Character.BoundaryMutation
plyA	ELynx.Data.Character.BoundaryMutation
plyB	ELynx.Data.Character.BoundaryMutation
plyI	ELynx.Data.Character.BoundaryMutation
plyN	ELynx.Data.Character.BoundaryMutation
poisson	ELynx.Data.MarkovProcess.AminoAcid
poissonCustom	ELynx.Data.MarkovProcess.AminoAcid
PopulationNames	ELynx.Export.Sequence.CountsFile
PopulationSize	ELynx.Data.Character.BoundaryMutation
Pos	ELynx.Export.Sequence.CountsFile
ProbMatrix	ELynx.Simulate.MarkovProcess
probMatrix	ELynx.Simulate.MarkovProcess
Protein	ELynx.Data.Alphabet.Alphabet
ProteinI	ELynx.Data.Alphabet.Alphabet
ProteinS	ELynx.Data.Alphabet.Alphabet
ProteinX	ELynx.Data.Alphabet.Alphabet
Q
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
R
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
randomSubSample	ELynx.Data.Sequence.MultiSequenceAlignment
RateMatrix	ELynx.Data.MarkovProcess.RateMatrix
S
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
scale
1 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.Data.MarkovProcess.MixtureModel
Sequence
1 (Type/Class)	ELynx.Data.Sequence.Sequence
2 (Data Constructor)	ELynx.Data.Sequence.Sequence
SequenceCharacters	ELynx.Data.Sequence.Sequence
sequenceListHeader	ELynx.Data.Sequence.Sequence
SequenceName	ELynx.Data.Sequence.Sequence
sequencesToFasta	ELynx.Export.Sequence.Fasta
sequenceToFasta	ELynx.Export.Sequence.Fasta
setDiagonal	ELynx.Data.MarkovProcess.RateMatrix
setPopulationSize	ELynx.Data.Character.BoundaryMutation
showCounts	ELynx.Data.Character.BoundaryMutation
showMSA	ELynx.Data.Sequence.MultiSequenceAlignment
showSequence	ELynx.Data.Sequence.Sequence
showSequenceList	ELynx.Data.Sequence.Sequence
simulateAndFlattenNSitesAlongTree	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlattenNSitesAlongTreeMixtureModel	ELynx.Simulate.MarkovProcessAlongTree
simulateNSitesAlongTree	ELynx.Simulate.MarkovProcessAlongTree
simulateNSitesAlongTreeMixtureModel	ELynx.Simulate.MarkovProcessAlongTree
Standard	ELynx.Data.Character.Codon
State
1 (Type/Class)	ELynx.Data.Character.BoundaryMutation
2 (Type/Class)	ELynx.Simulate.MarkovProcess
stateSpace	ELynx.Data.Character.BoundaryMutation
stateSpaceSize	ELynx.Data.Character.BoundaryMutation
StationaryDistribution	ELynx.Data.MarkovProcess.RateMatrix
stationaryDistribution	ELynx.Data.MarkovProcess.SubstitutionModel
std	ELynx.Data.Alphabet.Alphabet
Stop
1 (Data Constructor)	ELynx.Data.Character.AminoAcidS
2 (Data Constructor)	ELynx.Data.Character.AminoAcidI
subSample	ELynx.Data.Sequence.MultiSequenceAlignment
SubstitutionModel
1 (Type/Class)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Data Constructor)	ELynx.Data.MarkovProcess.PhyloModel
substitutionModel	ELynx.Data.MarkovProcess.SubstitutionModel
summarize
1 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.Data.MarkovProcess.MixtureModel
3 (Function)	ELynx.Data.MarkovProcess.PhyloModel
summarizeComponent	ELynx.Data.MarkovProcess.MixtureModel
summarizeGammaRateHeterogeneity	ELynx.Data.MarkovProcess.GammaRateHeterogeneity
summarizeMSA	ELynx.Data.Sequence.MultiSequenceAlignment
summarizeSequence	ELynx.Data.Sequence.Sequence
summarizeSequenceList	ELynx.Data.Sequence.Sequence
summarizeSequenceListBody	ELynx.Data.Sequence.Sequence
T
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.Nucleotide
6 (Data Constructor)	ELynx.Data.Character.NucleotideI
7 (Data Constructor)	ELynx.Data.Character.NucleotideX
toChar
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
toCharacters	ELynx.Data.Sequence.Sequence
toCountsFile	ELynx.Export.Sequence.CountsFile
toCVec	ELynx.Data.Alphabet.Character
toExchangeabilityMatrix	ELynx.Data.MarkovProcess.RateMatrix
toFrequencyData	ELynx.Data.Sequence.MultiSequenceAlignment
toIndex	ELynx.Data.Character.BoundaryMutation
toSequenceList	ELynx.Data.Sequence.MultiSequenceAlignment
toStandard	ELynx.Data.Character.Character
toStd	ELynx.Data.Alphabet.Alphabet
toString
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
totalRate
1 (Function)	ELynx.Data.MarkovProcess.RateMatrix
2 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
toWord
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
translate	ELynx.Data.Character.Codon
translateI	ELynx.Data.Character.Codon
translateSeq	ELynx.Data.Sequence.Translate
translateX	ELynx.Data.Character.Codon
trimSequence	ELynx.Data.Sequence.Sequence
U	ELynx.Data.Character.NucleotideI
UniversalCode	ELynx.Data.Character.Codon
unknown
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Alphabet
unnormalized	ELynx.Data.MarkovProcess.SubstitutionModel
unsafeFromList	ELynx.Data.Character.Codon
unsafeFromVec	ELynx.Data.Character.Codon
V
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
VertebrateMitochondrial	ELynx.Data.Character.Codon
W
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
wag	ELynx.Data.MarkovProcess.AminoAcid
wagCustom	ELynx.Data.MarkovProcess.AminoAcid
wagCustomUnnormalized	ELynx.Data.MarkovProcess.AminoAcid
Weight	ELynx.Data.MarkovProcess.MixtureModel
X	ELynx.Data.Character.AminoAcidI
Y
1 (Data Constructor)	ELynx.Data.Character.AminoAcidX
2 (Data Constructor)	ELynx.Data.Character.AminoAcidS
3 (Data Constructor)	ELynx.Data.Character.AminoAcidI
4 (Data Constructor)	ELynx.Data.Character.AminoAcid
5 (Data Constructor)	ELynx.Data.Character.NucleotideI
Z	ELynx.Data.Character.AminoAcidI