diff --git a/docs/src/index.md b/docs/src/index.md index f5577c2..117681e 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -4,28 +4,27 @@ CurrentModule = CodonMolecularEvolution # 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 ```