Contents
Index
elynx-seq-0.3.2: 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
Alphabet
ELynx.Data.Alphabet.Alphabet
alphabet
1 (Function)
ELynx.Data.Sequence.Sequence
2 (Function)
ELynx.Data.Sequence.Alignment
alphabetDescription
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
B
1 (Data Constructor)
ELynx.Data.Character.AminoAcidI
2 (Data Constructor)
ELynx.Data.Character.NucleotideI
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
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
Codon
1 (Type/Class)
ELynx.Data.Character.Codon
2 (Data Constructor)
ELynx.Data.Character.Codon
concat
1 (Function)
ELynx.Data.Sequence.Sequence
2 (Function)
ELynx.Data.Sequence.Alignment
concatAlignments
ELynx.Data.Sequence.Alignment
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
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
Description
ELynx.Data.Sequence.Sequence
description
ELynx.Data.Sequence.Sequence
descriptions
ELynx.Data.Sequence.Alignment
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
entropy
ELynx.Data.Alphabet.DistributionDiversity
equalLength
ELynx.Data.Sequence.Sequence
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
fromSequences
ELynx.Data.Sequence.Alignment
fromString
1 (Function)
ELynx.Data.Character.Character
2 (Function)
ELynx.Data.Alphabet.Character
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
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
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
iupac
1 (Function)
ELynx.Data.Character.Character
2 (Function)
ELynx.Data.Alphabet.Alphabet
J
ELynx.Data.Character.AminoAcidI
join
ELynx.Data.Sequence.Alignment
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
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
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.Sequence.Sequence
name
ELynx.Data.Sequence.Sequence
names
ELynx.Data.Sequence.Alignment
nameWidth
ELynx.Data.Sequence.Defaults
nSequences
ELynx.Data.Sequence.Alignment
Nucleotide
ELynx.Data.Character.Nucleotide
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
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
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
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
Standard
ELynx.Data.Character.Codon
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
summarize
1 (Function)
ELynx.Data.Sequence.Sequence
2 (Function)
ELynx.Data.Sequence.Alignment
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
toCVec
ELynx.Data.Alphabet.Character
toFrequencyData
ELynx.Data.Sequence.Alignment
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
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
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
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