Index

A
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.Nucleotide
6 (Data Constructor)	ELynx.Character.NucleotideI
7 (Data Constructor)	ELynx.Character.NucleotideX
Alignment
1 (Type/Class)	ELynx.Sequence.Alignment
2 (Data Constructor)	ELynx.Sequence.Alignment
all	ELynx.Alphabet.Alphabet
Alphabet	ELynx.Alphabet.Alphabet
alphabet
1 (Function)	ELynx.Sequence.Sequence
2 (Function)	ELynx.Sequence.Alignment
alphabetDescription	ELynx.Alphabet.Alphabet
AlphabetSpec
1 (Type/Class)	ELynx.Alphabet.Alphabet
2 (Data Constructor)	ELynx.Alphabet.Alphabet
alphabetSpec	ELynx.Alphabet.Alphabet
AminoAcid	ELynx.Character.AminoAcid
AminoAcidI	ELynx.Character.AminoAcidI
AminoAcidS	ELynx.Character.AminoAcidS
AminoAcidX	ELynx.Character.AminoAcidX
B
1 (Data Constructor)	ELynx.Character.AminoAcidI
2 (Data Constructor)	ELynx.Character.NucleotideI
body	ELynx.Sequence.Sequence
C
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.Nucleotide
6 (Data Constructor)	ELynx.Character.NucleotideI
7 (Data Constructor)	ELynx.Character.NucleotideX
Character
1 (Type/Class)	ELynx.Character.Character
2 (Type/Class)	ELynx.Alphabet.Character
CharacterI	ELynx.Character.Character
Characters	ELynx.Sequence.Sequence
characters	ELynx.Sequence.Sequence
CharacterX	ELynx.Character.Character
Codon
1 (Type/Class)	ELynx.Character.Codon
2 (Data Constructor)	ELynx.Character.Codon
concat
1 (Function)	ELynx.Sequence.Sequence
2 (Function)	ELynx.Sequence.Alignment
concatAlignments	ELynx.Sequence.Alignment
concatSequences	ELynx.Sequence.Sequence
convert	ELynx.Character.Character
countGaps	ELynx.Sequence.Alignment
countIUPACChars	ELynx.Sequence.Alignment
countUnknowns	ELynx.Sequence.Alignment
D
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
Description	ELynx.Sequence.Sequence
description	ELynx.Sequence.Sequence
descriptions	ELynx.Sequence.Alignment
distribution	ELynx.Sequence.Alignment
divergence	ELynx.Sequence.Divergence
DNA	ELynx.Alphabet.Alphabet
DNAI	ELynx.Alphabet.Alphabet
DNAX	ELynx.Alphabet.Alphabet
E
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
entropy	ELynx.Alphabet.DistributionDiversity
equalLength	ELynx.Sequence.Sequence
F
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
fasta	ELynx.Sequence.Import.Fasta
fastaSequence	ELynx.Sequence.Import.Fasta
fieldWidth	ELynx.Sequence.Defaults
filterColsConstant	ELynx.Sequence.Alignment
filterColsConstantSoft	ELynx.Sequence.Alignment
filterColsNoGaps	ELynx.Sequence.Alignment
filterColsOnlyStd	ELynx.Sequence.Alignment
filterColsStd	ELynx.Sequence.Alignment
filterLongerThan	ELynx.Sequence.Sequence
filterShorterThan	ELynx.Sequence.Sequence
filterStandard	ELynx.Sequence.Sequence
frequencyCharacters	ELynx.Alphabet.DistributionDiversity
FrequencyData	ELynx.Sequence.Alignment
fromByteString	ELynx.Sequence.Sequence
fromChar
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Character
fromCVec	ELynx.Alphabet.Character
fromSequences	ELynx.Sequence.Alignment
fromString
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Character
fromVecUnsafe	ELynx.Character.Codon
fromWord
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Character
G
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.Nucleotide
6 (Data Constructor)	ELynx.Character.NucleotideI
7 (Data Constructor)	ELynx.Character.NucleotideX
Gap
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.NucleotideI
5 (Data Constructor)	ELynx.Character.NucleotideX
gap
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Alphabet
H
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
hamming	ELynx.Sequence.Distance
header	ELynx.Sequence.Sequence
homoplasy	ELynx.Alphabet.DistributionDiversity
I
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
isGap
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Alphabet
isIUPAC
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Alphabet
isMember	ELynx.Alphabet.Alphabet
isStandard	ELynx.Character.Character
isStd	ELynx.Alphabet.Alphabet
isUnknown
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Alphabet
iupac
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Alphabet
J	ELynx.Character.AminoAcidI
join	ELynx.Sequence.Alignment
K
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
kEffEntropy
1 (Function)	ELynx.Alphabet.DistributionDiversity
2 (Function)	ELynx.Sequence.Alignment
kEffHomoplasy
1 (Function)	ELynx.Alphabet.DistributionDiversity
2 (Function)	ELynx.Sequence.Alignment
L
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
length
1 (Function)	ELynx.Sequence.Sequence
2 (Function)	ELynx.Sequence.Alignment
longest	ELynx.Sequence.Sequence
M
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
matrix	ELynx.Sequence.Alignment
N
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
Name	ELynx.Sequence.Sequence
name	ELynx.Sequence.Sequence
names	ELynx.Sequence.Alignment
nameWidth	ELynx.Sequence.Defaults
nSequences	ELynx.Sequence.Alignment
Nucleotide	ELynx.Character.Nucleotide
NucleotideI	ELynx.Character.NucleotideI
NucleotideX	ELynx.Character.NucleotideX
P
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
Protein	ELynx.Alphabet.Alphabet
ProteinI	ELynx.Alphabet.Alphabet
ProteinS	ELynx.Alphabet.Alphabet
ProteinX	ELynx.Alphabet.Alphabet
Q
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
R
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
randomSubSample	ELynx.Sequence.Alignment
S
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
Sequence
1 (Type/Class)	ELynx.Sequence.Sequence
2 (Data Constructor)	ELynx.Sequence.Sequence
sequencesToFasta	ELynx.Sequence.Export.Fasta
sequenceToFasta	ELynx.Sequence.Export.Fasta
Standard	ELynx.Character.Codon
std	ELynx.Alphabet.Alphabet
Stop
1 (Data Constructor)	ELynx.Character.AminoAcidS
2 (Data Constructor)	ELynx.Character.AminoAcidI
subSample	ELynx.Sequence.Alignment
summarize
1 (Function)	ELynx.Sequence.Sequence
2 (Function)	ELynx.Sequence.Alignment
summarizeSequences	ELynx.Sequence.Sequence
summaryLength	ELynx.Sequence.Defaults
summaryNSequences	ELynx.Sequence.Defaults
T
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.Nucleotide
6 (Data Constructor)	ELynx.Character.NucleotideI
7 (Data Constructor)	ELynx.Character.NucleotideX
toByteString	ELynx.Sequence.Sequence
toChar
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Character
toCVec	ELynx.Alphabet.Character
toFrequencyData	ELynx.Sequence.Alignment
toSequences	ELynx.Sequence.Alignment
toStandard	ELynx.Character.Character
toStd	ELynx.Alphabet.Alphabet
toString
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Character
toWord
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Character
translate	ELynx.Character.Codon
translateI	ELynx.Character.Codon
translateSeq	ELynx.Sequence.Translate
translateX	ELynx.Character.Codon
trim	ELynx.Sequence.Sequence
U	ELynx.Character.NucleotideI
UniversalCode	ELynx.Character.Codon
unknown
1 (Function)	ELynx.Character.Character
2 (Function)	ELynx.Alphabet.Alphabet
V
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
VertebrateMitochondrial	ELynx.Character.Codon
W
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
X	ELynx.Character.AminoAcidI
Y
1 (Data Constructor)	ELynx.Character.AminoAcidX
2 (Data Constructor)	ELynx.Character.AminoAcidS
3 (Data Constructor)	ELynx.Character.AminoAcidI
4 (Data Constructor)	ELynx.Character.AminoAcid
5 (Data Constructor)	ELynx.Character.NucleotideI
Z	ELynx.Character.AminoAcidI