Contents
Index
elynx-seq-0.0.1: Handle molecular sequences
A
B
C
D
E
F
G
H
I
J
K
L
M
N
P
Q
R
S
T
U
V
W
X
Y
Z
All
Index - S
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