ELynx.Data.Sequence.Alignment

Creation date: Thu Oct 4 18:40:18 2018.

This module is to be imported qualified.

Documentation

data Alignment

A collection of sequences.

Constructors

Alignment

Fields

• names :: [Name]
• descriptions :: [Description]
• alphabet :: Alphabet
• matrix :: Matrix Character

Instances

Eq Alignment

Defined in ELynx.Data.Sequence.Alignment

Methods

(==) :: Alignment -> Alignment -> Bool

(/=) :: Alignment -> Alignment -> Bool

Show Alignment

Defined in ELynx.Data.Sequence.Alignment

Methods

showsPrec :: Int -> Alignment -> ShowS

show :: Alignment -> String

showList :: [Alignment] -> ShowS

length :: Alignment -> Int

Number of sites.

nSequences :: Alignment -> Int

Number of sequences.

• Input, output

fromSequences :: [Sequence] -> Either String Alignment

Create Alignment from a list of Sequences.

toSequences :: Alignment -> [Sequence]

Conversion to list of Sequences.

summarize :: Alignment -> ByteString

Similar to summarizeSequenceList but with different Header.

• Manipulation

join :: Alignment -> Alignment -> Alignment

Join two Alignments vertically. That is, add more sequences to an alignment. See also concat.

concat :: Alignment -> Alignment -> Alignment

Concatenate two Alignments horizontally. That is, add more sites to an alignment. See also join.

concatAlignments :: [Alignment] -> Alignment

Concatenate a list of Alignments horizontally. See concat.

filterColsConstant :: Alignment -> Alignment

Only keep constant columns.

filterColsConstantSoft :: Alignment -> Alignment

Only keep constant columns, and constant columns with at least one standard character as well as any number of gaps or unknowns.

filterColsOnlyStd :: Alignment -> Alignment

Only keep columns with standard characters. Alignment columns with IUPAC characters are removed.

filterColsStd :: Double -> Alignment -> Alignment

Filter columns with proportion of standard character larger than given number.

filterColsNoGaps :: Alignment -> Alignment

Only keep columns without gaps or unknown characters.

• Analysis

type FrequencyData = Matrix Double

Frequency data; do not store the actual characters, but their frequencies. The matrix is of size N x K, where N is the number of sites, and K is the number of characters.

distribution :: FrequencyData -> [Double]

Calculate the distribution of characters.

toFrequencyData :: Alignment -> FrequencyData

Calculcate frequency of characters at each site of a multi sequence alignment.

kEffEntropy :: FrequencyData -> [Double]

Diversity analysis. See kEffEntropy.

kEffHomoplasy :: FrequencyData -> [Double]

Diversity analysis. See kEffEntropy.

countIUPACChars :: Alignment -> Int

Count the number of standard (i.e., not extended IUPAC) characters in the alignment.

countGaps :: Alignment -> Int

Count the number of gaps in the alignment.

countUnknowns :: Alignment -> Int

Count the number of unknown characters in the alignment.

• Sub sample

subSample :: [Int] -> Alignment -> Alignment

Sample the given sites from a multi sequence alignment.

randomSubSample :: PrimMonad m => Int -> Alignment -> Gen (PrimState m) -> m Alignment

Randomly sample a given number of sites of the multi sequence alignment.