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README.md

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 # FAVITES-Lite
-FAVITES-Lite: A lightweight framework for viral transmission and evolution simulation
+FAVITES-Lite is a lightweight framework for viral transmission and evolution simulation. It is a spin-off of [FAVITES](https://github.com/niemasd/FAVITES) that is designed to be much simpler and faster, but at the expense of reduced flexibility. FAVITES-Lite was designed to incorporate the just key functionality of FAVITES that most users require. In general, we strongly recommend using FAVITES-Lite instead of FAVITES for epidemic simulation projects.
+
+## Installation
+FAVITES-Lite is written in Python, but it calls many command-line tools. To install FAVITES-Lite itself, you can either download the latest [release](https://github.com/niemasd/FAVITES-Lite/releases), or you can clone this GitHub repository:
+
+```bash
+git clone https://github.com/niemasd/FAVITES-Lite.git
+```
+
+You must also install all of the FAVITES-Lite dependencies to your `PATH`:
+
+* [CoaTran](https://github.com/niemasd/CoaTran)
+* [GEMF_FAVITES](https://github.com/niemasd/GEMF)
+* [NiemaGraphGen](https://github.com/niemasd/NiemaGraphGen)
+* [Seq-Gen](https://github.com/rambaut/Seq-Gen)
+
+For convenience, you can also use the [FAVITES-Lite Docker image](https://hub.docker.com/r/niemasd/favites_lite), or you can refer to the [`Dockerfile`](https://github.com/niemasd/FAVITES-Lite/blob/main/Dockerfile#L12-L42) for installation commands.
+
+## Usage
+There are two primary components to FAVITES-Lite: the [Config Designer](config_designer.py) and the [FAVITES-Lite executable](favites_lite.py).
+
+### Config Designer
+The [Config Designer (`config_designer.py`)](config_designer.py) is a tool that helps users design a FAVITES-Lite configuration file for their unique simulation experiment design. Unlike the original FAVITES, in which users had to navigate the documentation to manually design a configuration file, the FAVITES-Lite Config Designer guides the user and includes detailed information about all model choices for all steps of the simulation workflow.
+
+To enter the Config Designer start page, which has a file navigator for creating a new config file or loading an existing one, simply execute the Config Designer without any arguments:
+
+```bash
+config_designer.py
+```
+
+If you already known the name of the new config file you wish to create or the existing config file you wish to view/modify, you can execute the Config Designer with the path to the desired config file as the only argument:
+
+```bash
+config_designer.py example/example.json
+```
+
+### FAVITES-Lite Executable
+The [FAVITES-Lite executable (`favites_lite.py`)](favites_lite.py) actually executes a given simulation experiment, and it can be used as follows:
+
+```
+usage: favites_lite.py [-h] -c CONFIG -o OUTPUT [--overwrite] [--quiet] [--version]
+
+  -h, --help                   show this help message and exit
+  -c CONFIG, --config CONFIG   FAVITES-Lite Config File
+  -o OUTPUT, --output OUTPUT   Output Directory
+  --overwrite                  Overwrite output directory if it exists (default: False)
+  --quiet                      Suppress Log Messages (default: False)
+  --version                    Show FAVITES-Lite version (default: False)
+```