Contents
Index
elynx-seq-0.1.0: Handle molecular sequences
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