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nossleinad authored Jun 14, 2024
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# CodonMolecularEvolution

### A Julia package for popular and new codon models of molecular evolution.

Documentation for [CodonMolecularEvolution](https://github.com/MurrellGroup/CodonMolecularEvolution.jl).

Descendant of [MolecularEvolution.jl](https://github.com/MurrellGroup/MolecularEvolution.jl), specializing in codon models.

### A Julia package that contains a collection of popular/(state of the art) codon model methods.

CodonMolecularEvolution.jl leverages the MolecularEvolution.jl framework to provide a performant interface to some codon model methods that are used for phylogenetic analysis.

### Collection of codon model methods
- [difFUBAR](@ref): Scalable Bayesian comparison of selection pressure
- Perform a site-wise comparison of evolutionary pressure between two selected sets of branches.
- Authors: Hassan Sadiq, Venkatesh Kumar, and Ben Murrell (original model development), Patrick Truong (benchmarking), Maximilian Danielsson (performance optimization).

### Design principles
- Specificity
- We keep our implementations on a high level of abstraction and let `MolecularEvolution.jl` take care of the low-level behaviour.
- User-facing
- Users with no Julia experience should be able to run these models.
- Scalability
- Our exported codon model methods should scale to large, real-world datasets. To keep the memory footprint down, we use `MolecularEvolution.jl`s `LazyPartition` when possible.
- Models should scale to large, real-world datasets. To keep the memory footprint down, we use `MolecularEvolution.jl`s `LazyPartition` when possible.
- Performance
- While scalability takes precedence over speed?, we try to maintain competitive runtimes by using e.g. computational shortcuts and parallelization whenever we can.
- We try to maintain competitive runtimes by using e.g. computational shortcuts and parallelization whenever we can.

### Authors
Ben decides what to put here.
### Package Authors and Maintainers
Maximilian Danielsson and Ben Murrell. Authors for specific models listed above.

```@index
```
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