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README.md

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-# hcvGlue
-This is a [GLUE](http://glue-tools.cvr.gla.ac.uk/) project for Hepatitis C virus.
+# HCV-GLUE: Phylogenomic Analysis of Hepatitis C Virus
+
+## Overview
+
+HCV-GLUE is a sequence-oriented resource for comparative genomic analysis of hepatitis C virus (HCV), developed using the [GLUE](https://github.com/giffordlabcvr/gluetools) software framework.
+
+This **HCV-GLUE** base project can be extended with additional layers, openly availabe via GitHub, including:
+
+  - **[NCBI-HCV-GLUE](https://github.com/giffordlabcvr/NCBI-HCV-GLUE)**: extends HCV-GLUE through the incorporation of all HCV sequence data published in NCBI GenBank.
+  - **[HCV-GLUE-WEB](https://github.com/giffordlabcvr/HCV-GLUE-WEB)**: a web interface that can be used to create a HCV-GLUE web-server.
+
+A web instance of HCV-GLUE incorporating both these extension layers is hosted by the University of Glasgow, and can be accessed here **[here](http://hcv-glue.cvr.gla.ac.uk/)**.
+
+In HCV-GLUE, HCV sequence data are richly annotated with gene features and isolate-associated information. HCV-GLUE also contains reference sequences for all HCV genotypes and subtypes, as well as heirarchically ordered multiple sequence alignments.
+
+## Table of Contents
+
+- [Overview](#overview)
+- [Key Features](#key-features)
+- [Installation](#installation)
+- [Usage](#usage)
+- [Contributing](#contributing)
+- [License](#license)
+- [Contact](#contact)
+
+## Key Features
+
+- **GLUE Framework Integration**: Built on the GLUE software framework, HCV-GLUE offers an extensible platform for efficient, standardized, and reproducible computational genomic analysis of influenza viruses.
+
+- **Phylogenetic Structure**: The data in HCV-GLUE is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships easily.
+
+- **Automated Updates**: HCV-GLUE provides an automatically-updated collection of influenza sequence data, ensuring users have access to the latest information for their analyses.
+
+- **Rich Annotations**: Each sequence is annotated with gene features, enabling rigorous comparative genomic analysis related to conservation, adaptation, structural context, and genotype-to-phenotype associations.
+
+- **Automated Genotyping**: HCV-GLUE can perform automated genotyping of HCV sequences (including subgenomic sequences) using GLUE's maximum likelihood clade assignment (MLCA) algorithm, as described [here](https://doi.org/10.1186/s12859-018-2459-9).
+
+- **Web user interface**: The [HCV-GLUE-WEB](https://github.com/giffordlabcvr/HCV-GLUE-WEB) extension project defines a web user interface that supports online browsing of the HCV-GLUE sequence database, and provides web access to an in-built sequence analysis tool (provides genotyping, analysis and visualisation of submitted FASTA sequences).
+
+
+## Installation
+
+If you have not done so already, install the GLUE software framework by following the [installation instructions](http://glue-tools.cvr.gla.ac.uk/#/installation) on the GLUE web site: 
+
+Note the HCV-GLUE project has a layered structure. This approach simplifies project management because it allows data items that are likely to be used across a wide range of analysis contexts to be maintained separately from those only required for more specialized purposes. The ‘base’ layer of HCV-GLUE contains only a minimal set of essential data items required for comparative analysis.
+
+To build the base (or 'core') project, download the HCV-GLUE repository, navigate into the top-level directory, and start the GLUE command line interpreter, e.g.:
+
+```
+rob$ gluetools.sh
+
+GLUE Version 1.1.107
+Copyright (C) 2015-2020 The University of Glasgow
+This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you
+are welcome to redistribute it under certain conditions. For details see
+GNU Affero General Public License v3: http://www.gnu.org/licenses/
+
+Mode path: /
+GLUE>
+```
+
+At the GLUE command prompt, run the 'buildCoreProject.glue' file as follows:
+
+`GLUE> run file hcvProject.glue`
+
+This will build the base project, which contains a minimal set of HCV 'reference' sequences. The base project can be extended to incorporate all HCV sequences in GenBank by downloading the extension project [NCBI-HCV-GLUE](https://github.com/giffordlabcvr/NCBI-HCV-GLUE).
+
+## Usage
+
+GLUE contains an interactive command line environment focused on the development and use of GLUE projects by bioinformaticians. This provides a range of productivity-oriented features such as automatic command completion, command history and interactive paging through tabular data. 
+
+For detailed instructions on how to use HCV-GLUE for your comparative genomic analysis, refer to the GLUE software environment's [reference documentation](http://glue-tools.cvr.gla.ac.uk/).
+
+## Contributing
+
+We welcome contributions from the community! If you're interested in contributing to HCV-GLUE, please review our [Contribution Guidelines](./md/CONTRIBUTING.md).
+
+[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](./md/code_of_conduct.md) 
+
+## License
+
+The project is licensed under the [GNU Affero General Public License v. 3.0](https://www.gnu.org/licenses/agpl-3.0.en.html)
+
+## Contact
+
+For questions, issues, or feedback, please contact us at [gluetools@gmail.com](mailto:gluetools@gmail.com) or open an issue on the [GitHub repository](https://github.com/giffordlabcvr/HCV-GLUE/issues).
 
-A GUI version of HCV-GLUE is available [here](http://hcv-glue.cvr.gla.ac.uk/).