elynx-seq-0.6.0.0: 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
allELynx.Data.Alphabet.Alphabet
AlphabetELynx.Data.Alphabet.Alphabet
alphabet 
1 (Function)ELynx.Data.Sequence.Sequence
2 (Function)ELynx.Data.Sequence.Alignment
alphabetDescriptionELynx.Data.Alphabet.Alphabet
AlphabetSpec 
1 (Type/Class)ELynx.Data.Alphabet.Alphabet
2 (Data Constructor)ELynx.Data.Alphabet.Alphabet
alphabetSpecELynx.Data.Alphabet.Alphabet
AminoAcidELynx.Data.Character.AminoAcid
AminoAcidIELynx.Data.Character.AminoAcidI
AminoAcidSELynx.Data.Character.AminoAcidS
AminoAcidXELynx.Data.Character.AminoAcidX
B 
1 (Data Constructor)ELynx.Data.Character.AminoAcidI
2 (Data Constructor)ELynx.Data.Character.NucleotideI
bodyELynx.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
CharacterIELynx.Data.Character.Character
CharactersELynx.Data.Sequence.Sequence
charactersELynx.Data.Sequence.Sequence
CharacterXELynx.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
concatAlignmentsELynx.Data.Sequence.Alignment
concatSequencesELynx.Data.Sequence.Sequence
convertELynx.Data.Character.Character
countGapsELynx.Data.Sequence.Alignment
countIUPACCharsELynx.Data.Sequence.Alignment
countUnknownsELynx.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
DescriptionELynx.Data.Sequence.Sequence
descriptionELynx.Data.Sequence.Sequence
descriptionsELynx.Data.Sequence.Alignment
distributionELynx.Data.Sequence.Alignment
DNAELynx.Data.Alphabet.Alphabet
DNAIELynx.Data.Alphabet.Alphabet
DNAXELynx.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
entropyELynx.Data.Alphabet.DistributionDiversity
equalLengthELynx.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
fastaELynx.Import.Sequence.Fasta
fastaSequenceELynx.Import.Sequence.Fasta
fieldWidthELynx.Data.Sequence.Defaults
filterColsConstantELynx.Data.Sequence.Alignment
filterColsConstantSoftELynx.Data.Sequence.Alignment
filterColsNoGapsELynx.Data.Sequence.Alignment
filterColsOnlyStdELynx.Data.Sequence.Alignment
filterColsStdELynx.Data.Sequence.Alignment
filterLongerThanELynx.Data.Sequence.Sequence
filterShorterThanELynx.Data.Sequence.Sequence
filterStandardELynx.Data.Sequence.Sequence
frequencyCharactersELynx.Data.Alphabet.DistributionDiversity
FrequencyDataELynx.Data.Sequence.Alignment
fromByteStringELynx.Data.Sequence.Sequence
fromChar 
1 (Function)ELynx.Data.Character.Character
2 (Function)ELynx.Data.Alphabet.Character
fromCVecELynx.Data.Alphabet.Character
fromSequencesELynx.Data.Sequence.Alignment
fromString 
1 (Function)ELynx.Data.Character.Character
2 (Function)ELynx.Data.Alphabet.Character
fromVecUnsafeELynx.Data.Character.Codon
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
hammingELynx.Data.Sequence.Distance
headerELynx.Data.Sequence.Sequence
homoplasyELynx.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
isMemberELynx.Data.Alphabet.Alphabet
isStandardELynx.Data.Character.Character
isStdELynx.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
JELynx.Data.Character.AminoAcidI
joinELynx.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
longestELynx.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
matrixELynx.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
NameELynx.Data.Sequence.Sequence
nameELynx.Data.Sequence.Sequence
namesELynx.Data.Sequence.Alignment
nameWidthELynx.Data.Sequence.Defaults
nSequencesELynx.Data.Sequence.Alignment
NucleotideELynx.Data.Character.Nucleotide
NucleotideIELynx.Data.Character.NucleotideI
NucleotideXELynx.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
ProteinELynx.Data.Alphabet.Alphabet
ProteinIELynx.Data.Alphabet.Alphabet
ProteinSELynx.Data.Alphabet.Alphabet
ProteinXELynx.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
randomSubSampleELynx.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
sequencesToFastaELynx.Export.Sequence.Fasta
sequenceToFastaELynx.Export.Sequence.Fasta
StandardELynx.Data.Character.Codon
stdELynx.Data.Alphabet.Alphabet
Stop 
1 (Data Constructor)ELynx.Data.Character.AminoAcidS
2 (Data Constructor)ELynx.Data.Character.AminoAcidI
subSampleELynx.Data.Sequence.Alignment
summarize 
1 (Function)ELynx.Data.Sequence.Sequence
2 (Function)ELynx.Data.Sequence.Alignment
summarizeSequencesELynx.Data.Sequence.Sequence
summaryLengthELynx.Data.Sequence.Defaults
summaryNSequencesELynx.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
toByteStringELynx.Data.Sequence.Sequence
toChar 
1 (Function)ELynx.Data.Character.Character
2 (Function)ELynx.Data.Alphabet.Character
toCVecELynx.Data.Alphabet.Character
toFrequencyDataELynx.Data.Sequence.Alignment
toSequencesELynx.Data.Sequence.Alignment
toStandardELynx.Data.Character.Character
toStdELynx.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
translateELynx.Data.Character.Codon
translateIELynx.Data.Character.Codon
translateSeqELynx.Data.Sequence.Translate
translateXELynx.Data.Character.Codon
trimELynx.Data.Sequence.Sequence
UELynx.Data.Character.NucleotideI
UniversalCodeELynx.Data.Character.Codon
unknown 
1 (Function)ELynx.Data.Character.Character
2 (Function)ELynx.Data.Alphabet.Alphabet
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
VertebrateMitochondrialELynx.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
XELynx.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
ZELynx.Data.Character.AminoAcidI