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link: https://github.com/MurrellGroup/MolecularEvolution.jl
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features:
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- title: Flexible Model Development
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details: Create custom evolutionary models by defining how your new (or already existing) probability distributions evolve along a branch, and get likelihood calculations (and much more) for free! • Mix and match different models on the same phylogeny.
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details: Create custom evolutionary models by defining how a process evolves along a branch and get likelihood calculations (and much more) for free! • Mix and match different models on the same phylogeny.
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link: /framework
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- title: Rich Model Library
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details: Codon, AA, nucleotide and generic discrete character models as well as continuous Brownian motion in 1D. Site- and branch-wise mixture models and more.
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- title: Model Library
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details: Nucleotide, AA, Codon, and generic discrete character models • Continuous models (eg. Brownian motion) • Site- and branch-wise mixture models and more.
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link: /models
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- title: Powerful Tree Operations
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details: Optimize model parameters, branch lengths and root state/location. Perform tree rearrangements (NNI). The above can also be made in the Bayesian framework by sampling over posterior tree and parameter spaces with MCMC. • Infer ancestral states.
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- title: Tree Operations
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details: Optimize model parameters, branch lengths, tree topology (NNI), and root position for maximum likelihood inference • Sample from the model and tree posterior with MCMC for Bayesian inference • Infer ancestral states.
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link: /optimization
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- title: Simulation Tools
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details: Generate phylogenies using e.g. coalescent and logistic growth processes, and simulate both sequence evolution and continuous trait evolution on those trees.
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details: Sample from a range of realistic phylogenies using a flexible coalescent process • Simulate discrete and continuous data under any model over a simulated or imported phylogeny.
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link: /simulation
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