treesimulator 0.0.1

Simulation of rooted phylogenetic trees following an epidemiological model.

# Treesimulator

Simulates trees with given models.

## Naive-treated model 2 compartments: * treated, i.e. treatment-experienced * naive, i.e. treatment-naive

5 parameters: * $mu$, treatment rate (changes the compartment from naive to treated, the change happens along a tree branch) * $lambda_n$, transmission rate of naive individuals (corresponds to an internal node, the recipient is naive) * $lambda_t$, transmission rate of treated individuals (corresponds to an internal node, the recipient is naive), $lambda_t less lambda_n$ * $psi_n$, sampling rate of naive individuals (a tip of the tree), $psi_n less lambda_n$ * $psi_t$, sampling rate of treated individuals (a tip of the tree)

## Installation To install treesimulator: `bash pip3 install treesimulator `

## Usage To simulate a tree with 200 tips under naive-treated model, with $mu = .3, lambda_n = 1, lambda_t = .2, psi_n = .25, psi_t = .1$, and save it to a file tree.nwk: `bash treesimulator --n_tips 200 --rates .3 1 .2 .25 .1 --nwk tree.nwk `