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+# Getting Started
+
+A [video tutorial](https://youtu.be/dOwkInn6eDw) covering the instructions below is also available.
+
+### <a name="system-requirements"></a>System Requirements
+
+* JDK [17](https://www.oracle.com/java/technologies/downloads/#jdk17-windows)+
+   * A `JAVA_HOME` environment variable pointing to your JDK, or the Java executable in your PATH
+* [Gradle](https://gradle.org/install/) (included)
+
+### <a name="build-run"></a>Build & Run
+
+The easiest way to run the program on Windows is by using the executable file located in the [releases](https://github.com/VerisimilitudeX/DNAnalyzer/releases/latest) section to install the program, build gradle and run the GUI.
+
+* We use [Gradle](https://gradle.org) for building. The Gradle wrapper takes care of downloading dependencies, testing, compiling, linking, and packaging the code.
+<details>
+
+<summary>Windows</summary>
+
+The easiest way to run the program on Windows is by using the executable file located in the [releases](https://github.com/VerisimilitudeX/DNAnalyzer/releases/latest) section to install the program, build gradle and run the GUI.
+
+```pwsh
+.\gradlew build
+```
+
+### <a name="usage"></a>Usage
+
+```pwsh
+<executable> <arguments>
+```
+
+#### <a name="executable"></a>Executable
+
+```pwsh
+java -jar build/libs/DNAnalyzer.jar
+```
+
+#### <a name="arguments"></a>Arguments
+
+DNAnalyzer uses CLI arguments instead of `stdin`. For example, you can do:
+
+```pwsh
+assets/dna/random/dnalong.fa --amino=arg --min=16450 --max=520218 -r
+```
+
+### <a name="example"></a>Example
+
+```pwsh
+java -jar build/libs/DNAnalyzer.jar assets/dna/random/dnalong.fa --amino=ser --min=16450 --max=520218 -r
+```
+
+#### <a name="gradle-run"></a>Gradle Run
+
+If you prefer, you can also run it directly from Gradle:
+
+```pwsh
+.\gradlew run --args="assets/dna/random/dnalong.fa --amino=ser --min=10 --max=100"
+```
+
+#### <a name="gui"></a>GUI
+
+DNAnalyzer also comes with a (very basic) GUI; to start DNAnalyzer with the GUI, run:
+
+```pwsh
+.\gradlew run --args="--gui assets/dna/random/dnalong.fa"
+```
+
+Then:
+
+* Enter the file name of the DNA file in the text field
+* Set min and max
+* Click analyze
+
+* Note: Ensure you have Java [17](https://www.oracle.com/java/technologies/downloads/#java17) or higher installed and a `JAVA_HOME` path variable set for the program to function correctly!
+
+
+The results of your analysis will be shown in the right pane.
+
+</details>
+
+<details>
+      <summary>Linux & macOS</summary>
+
+
+### <a name="features"></a>DNAnalyzer & Java Download
+
+To run DNAnaylzer on Linux, you'll need to download the DNAnalyzer source code and download and install Java 17.
+
+First, download the zip or tar.gz file from [DNAnalyzer releases](https://github.com/VerisimilitudeX/DNAnalyzer/releases/latest) and unzip it using the native utility. 
+
+Then, download [Java 17](https://www.oracle.com/ca-en/java/technologies/downloads/#java17), find the download at https://www.oracle.com/ca-en/java/technologies/downloads/#java17, ensure you choose the Linux option and get the one for your correct processor architecture.
+
+### Java installation
+
+```bash
+wget https://download.oracle.com/java/17/latest/jdk-17_linux-x64_bin.tar.gz
+```
+Next, unzip it.
+
+```bash
+tar -xvzf jdk-17_linux-x64_bin.tar.gz
+```
+Then map the `JAVA_HOME` path. Fill it in with your JAVA directory where JAVA is unzipped.
+```bash
+export JAVA_HOME="{YOUR JAVA DIRECTORY HERE}/jdk-17.0.7" && export PATH=$JAVA_HOME/bin:$PATH
+```
+<details>
+<summary>Example of a full path command.</summary>
+
+```bash
+export JAVA_HOME="/workspaces/DNAnalyzer/jdk-17.0.7"
+```
+
+</details>
+
+```bash
+./gradlew build
+```
+If you see `Task :compileJava FAILED`, the program cannot find your Java installation. You may need to export your JAVA_HOME path again.
+
+## OpenAI API Key
+We use GPT-4 API to display the results of the analysis. To use the API, you'll need to get an API key from OpenAI. You can get one [here](https://platform.openai.com/). **Note, this is an optional step.** If you don't want to use the API, you can still use the program, but you won't be able to see the results of the analysis.
+
+To set the API key on Linux or macOS, run `export OPENAI_API_KEY=sk-xxxxxxxxxxxxxxxxxxxxxxxx` where `sk-xxxxxxxxxxxxxxxxxxxxxxxx` is your API key.
+
+For Windows, use `setx OPENAI_API_KEY=sk-xxxxxxxxxxxxxxxxxxxxxxxx` instead.
+
+
+### Usage
+
+```bash
+<executable> <arguments>
+```
+
+#### Executable
+
+```pwsh
+java -jar build/libs/DNAnalyzer.jar
+```
+
+#### Arguments
+
+DNAnalyzer uses CLI arguments instead of `stdin`. For example, you can do:
+
+```bash
+assets/dna/random/dnalong.fa --amino=arg --min=16450 --max=520218 -r
+```
+
+### Example
+
+```pwsh
+java -jar build/libs/DNAnalyzer.jar assets/dna/random/dnalong.fa --amino=ser --min=16450 --max=520218 -r
+```
+
+#### Gradle Run
+
+If you prefer, you can also run it directly from Gradle:
+
+```pwsh
+./gradlew run --args="assets/dna/random/dnalong.fa --amino=ser --min=10 --max=100"
+```
+
+#### GUI
+
+DNAnalyzer also comes with a (very basic) GUI; to start DNAnalyzer with the GUI, run:
+
+```pwsh
+./gradlew run --args="--gui assets/dna/random/dnalong.fa"
+```
+
+Then:
+
+* Enter the file name of the DNA file in the text field
+* Set min and max
+* Click analyze
+
+
+The results of your analysis will be shown in the right pane.
+</details>
+
+
+
+#### Available Commands
+
+```py
+
+
+Usage: DNAnalyzer [-hrV] --amino=<aminoAcid> [--find=<proteinFile>]
+                  [--max=<maxCount>] [--min=<minCount>] DNA
+A program to analyze DNA sequences.
+      DNA                    The FASTA file to be analyzed.
+      --amino=<aminoAcid>    The amino acid representing the start of a gene.
+      --find=<proteinFile>   The DNA sequence to be found within the FASTA file.
+  -h, --help                 Show this help message and exit.
+      --max=<maxCount>       The maximum count of the reading frame.
+      --min=<minCount>       The minimum count of the reading frame.
+  -r, --reverse              Reverse the DNA sequence before processing.
+  -V, --version              Print version information and exit.
+```
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