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
Alignment
1 (Type/Class)	ELynx.Data.Sequence.Alignment
2 (Data Constructor)	ELynx.Data.Sequence.Alignment
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
3 (Function)	ELynx.Data.Sequence.Alignment
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
body	ELynx.Data.Sequence.Sequence
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
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
concat
1 (Function)	ELynx.Data.Sequence.Sequence
2 (Function)	ELynx.Data.Sequence.Alignment
concatAlignments	ELynx.Data.Sequence.Alignment
concatenate	ELynx.Data.MarkovProcess.MixtureModel
concatSequences	ELynx.Data.Sequence.Sequence
convert	ELynx.Data.Character.Character
countGaps	ELynx.Data.Sequence.Alignment
countIUPACChars	ELynx.Data.Sequence.Alignment
countUnknowns	ELynx.Data.Sequence.Alignment
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
description	ELynx.Data.Alphabet.Alphabet
distribution	ELynx.Data.Sequence.Alignment
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, ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
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
fieldWidth	ELynx.Data.Sequence.Defaults
filterColsNoGaps	ELynx.Data.Sequence.Alignment
filterColsOnlyStd	ELynx.Data.Sequence.Alignment
filterColsStd	ELynx.Data.Sequence.Alignment
filterLongerThan	ELynx.Data.Sequence.Sequence
filterShorterThan	ELynx.Data.Sequence.Sequence
filterStandard	ELynx.Data.Sequence.Sequence
frequencyCharacters	ELynx.Data.Alphabet.DistributionDiversity
FrequencyData	ELynx.Data.Sequence.Alignment
fromByteString	ELynx.Data.Sequence.Sequence
fromChar
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
fromCVec	ELynx.Data.Alphabet.Character
fromExchangeabilityMatrix	ELynx.Data.MarkovProcess.RateMatrix
fromIndexWith	ELynx.Data.Character.BoundaryMutation
fromSequences	ELynx.Data.Sequence.Alignment
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
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
header	ELynx.Data.Sequence.Sequence
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
join	ELynx.Data.Sequence.Alignment
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.Alignment
kEffHomoplasy
1 (Function)	ELynx.Data.Alphabet.DistributionDiversity
2 (Function)	ELynx.Data.Sequence.Alignment
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
length
1 (Function)	ELynx.Data.Sequence.Sequence
2 (Function)	ELynx.Data.Sequence.Alignment
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
matrix	ELynx.Data.Sequence.Alignment
MixtureModel
1 (Type/Class)	ELynx.Data.MarkovProcess.MixtureModel
2 (Data Constructor)	ELynx.Data.MarkovProcess.MixtureModel
3 (Data Constructor)	ELynx.Data.MarkovProcess.PhyloModel
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
1 (Type/Class)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Type/Class)	ELynx.Data.Sequence.Sequence
name
1 (Function)	ELynx.Data.MarkovProcess.SubstitutionModel
2 (Function)	ELynx.Data.MarkovProcess.MixtureModel
3 (Function)	ELynx.Data.Sequence.Sequence
names	ELynx.Data.Sequence.Alignment
nameWidth	ELynx.Data.Sequence.Defaults
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
nSequences	ELynx.Data.Sequence.Alignment
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
1 (Type/Class)	ELynx.Import.MarkovProcess.EDMModelPhylobayes
2 (Type/Class)	ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
3 (Type/Class)	ELynx.Import.Sequence.Fasta
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.Alignment
RateMatrix	ELynx.Data.MarkovProcess.RateMatrix
rateMatrix	ELynx.Data.MarkovProcess.SubstitutionModel
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
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
simulate	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlatten	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlattenMixtureModel	ELynx.Simulate.MarkovProcessAlongTree
simulateAndFlattenMixtureModelPar	ELynx.Simulate.MarkovProcessAlongTree
simulateMixtureModel	ELynx.Simulate.MarkovProcessAlongTree
siteprofiles	ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
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.Alignment
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
4 (Function)	ELynx.Data.Sequence.Sequence
5 (Function)	ELynx.Data.Sequence.Alignment
summarizeComponent	ELynx.Data.MarkovProcess.MixtureModel
summarizeGammaRateHeterogeneity	ELynx.Data.MarkovProcess.GammaRateHeterogeneity
summarizeSequences	ELynx.Data.Sequence.Sequence
summaryLength	ELynx.Data.Sequence.Defaults
summaryNSequences	ELynx.Data.Sequence.Defaults
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
toByteString	ELynx.Data.Sequence.Sequence
toChar
1 (Function)	ELynx.Data.Character.Character
2 (Function)	ELynx.Data.Alphabet.Character
toCountsFile	ELynx.Export.Sequence.CountsFile
toCVec	ELynx.Data.Alphabet.Character
toExchangeabilityMatrix	ELynx.Data.MarkovProcess.RateMatrix
toFrequencyData	ELynx.Data.Sequence.Alignment
toIndex	ELynx.Data.Character.BoundaryMutation
toSequences	ELynx.Data.Sequence.Alignment
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
trim	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