https://github.com/biojulia/substitutionmodels.jl

Biological Sequence Substitution Models for Julia
https://github.com/biojulia/substitutionmodels.jl

bioinformatics julia phylogenetics substitution-models

Last synced: about 1 month ago
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Biological Sequence Substitution Models for Julia

• Host: GitHub
• URL: https://github.com/biojulia/substitutionmodels.jl
• Owner: BioJulia
• License: other
• Created: 2017-07-22T17:15:14.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2023-04-23T14:34:08.000Z (over 1 year ago)
• Last Synced: 2024-10-30T01:36:59.348Z (about 2 months ago)
• Topics: bioinformatics, julia, phylogenetics, substitution-models
• Language: Julia
• Homepage:
• Size: 542 KB
• Stars: 17
• Watchers: 13
• Forks: 7
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.md
  • Code of conduct: CODE_OF_CONDUCT.md

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README

        
# SubstitutionModels.jl

**Release status:**

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3988662.svg)](https://doi.org/10.5281/zenodo.3988662)

[![Latest Release](https://img.shields.io/github/release/BioJulia/SubstitutionModels.jl.svg)](https://github.com/BioJulia/SubstitutionModels.jl/releases/latest)

[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/SubstitutionModels.jl/blob/master/LICENSE)

[![](https://img.shields.io/badge/docs-stable-blue.svg)](https://BioJulia.github.io/SubstitutionModels.jl/stable)

![BioJulia maintainer: jangevaare](https://img.shields.io/badge/BioJulia%20Maintainer-jangevaare-orange.svg)

**Development status:**

[![test-lts](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/test-lts.yml/badge.svg)](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/test-lts.yml)

[![test-stable](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/test-stable.yml/badge.svg)](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/test-stable.yml)

[![test-nightly](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/test-nightly.yml/badge.svg)](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/test-nightly.yml)

[![codecov.io](http://codecov.io/github/BioJulia/SubstitutionModels.jl/coverage.svg?branch=master)](http://codecov.io/github/BioJulia/SubstitutionModels.jl?branch=master)

[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://BioJulia.github.io/SubstitutionModels.jl/latest)

## Description

SubstitutionModels.jl provides facilities to model the substitution process of

biological sequences. Such models are essential for the analysis of sequence

evolution, phylogenetics, and simulation.

We first aim to provide the most common substitution models

used in the literature, but aim to build an extendable framework using julia's

type system and traits, so as custom model types can be created and used.

## Installation

The current release version can be installed

from the Julia REPL:

```julia

using Pkg

Pkg.add("SubstitutionModels")

```

## Contributing and Questions

We appreciate contributions from users including reporting bugs, fixing issues,

improving performance and adding new features.

Please go to the [contributing section of the documentation](http://biojulia.dev/Contributing/latest/)

for more information.

If you have a question about

contributing or using this package, you are encouraged to use the

[Bio category of the Julia discourse

site](https://discourse.julialang.org/c/domain/bio).