Q package:elynx-seq

Handle molecular sequences Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at https://github.com/dschrempf/elynx.

frequencyCharacters :: (Vector v Character, Vector v Int, Vector v Double) => AlphabetSpec -> v Character -> v Double

elynx-seq ELynx.Alphabet.DistributionDiversity

For a given code vector of characters, calculate frequency of characters. The input vector has arbitrary length (most often the number of sequences in an alignment), the length of the output vector is the number of characters in the alphabet.

type FrequencyData = Matrix Double

elynx-seq ELynx.Sequence.Alignment

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.

fromSequences :: [Sequence] -> Either String Alignment

elynx-seq ELynx.Sequence.Alignment

Create Alignment from a list of Sequences.

nSequences :: Alignment -> Int

elynx-seq ELynx.Sequence.Alignment

Number of sequences.

toFrequencyData :: Alignment -> FrequencyData

elynx-seq ELynx.Sequence.Alignment

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

toSequences :: Alignment -> [Sequence]

elynx-seq ELynx.Sequence.Alignment

Conversion to list of Sequences.