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PierreBarrat authored Oct 1, 2024
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://PierreBarrat.github.io/BioSequenceMappings.jl/dev/)

The aim of the package is to facilitate the task of converting biological sequences (nucleotides, amino acids) to integers or to onehot representation.
It also provides simple function to manipulate alignments or to compute simple statistics.
It also provides simple functions to manipulate alignments or to compute simple statistics.

*Note*: I do not frequently use the onehot format, so for now it is not documented / not well tested. I'll develop it more when I get the time.

*Note*: The package is not aimed at being highly computationally efficient when dealing with sequences. The purpose is simply to help interfacing with other algorithms (I have DCA-like models in mind). If you are dealing with very large alignments and very large sequences, it is possible that this does not fit your needs.

## Installation

From a Julia session:
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f1 = site_specific_frequencies(A)
non_gapped_colums = findall(j -> f1[gap_digit, j] <= 0.05, 1:size(f1, 2))
B = Alignment(A.data[non_gapped_colums, :], A.alphabet; A.names) # sequences are stored as columns
```
```

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