Welcome to the GLUE User Guide!

GLUE (Genes Linked by Underlying Evolution) is an open, integrated software toolkit implemented in Java™. It is designed to facilitate the storage, management, and analysis of sequence data, offering researchers a powerful platform for genomic investigations.

GLUE provides a framework for the development of sequence data-oriented 'projects' that focus on specific genome features or small genomes (e.g., viral genomes). These projects encompass the data items necessary for conducting comparative genomics investigations, including sequences, genome feature annotations, alignments, phylogenies, and any other relevant data.

This guide is designed to help new users explore the full range of GLUE’s capabilities, from mastering basic commands to leveraging advanced scripting techniques. It also provides context regarding (i) the vision for GLUE and its foundation in open science, and (ii) the development of GLUE and its contribution to fostering collaborative research.

• Evolutionary Data Organisation: Stored nucleotide sequence alignments are organised along evolutionary lines, facilitating comparative genomics.

• Customizable Bioinformatics Workflows: GLUE includes integrations with standard bioinformatics tools such as BLAST, RAxML, and MAFFT, and users can create custom analysis workflows tailored to specific research needs, from simple analyses to complex pipelines.

• Flexible Data Schema: The underlying data schema can be extended to represent additional biological, epidemiological, or clinical data. GLUE allows custom annotations, metadata integration, and comprehensive data queries through its powerful command layer.

• Reference-Constrained Alignments: GLUE offers robust handling of reference-constrained alignments, capturing coding features at the nucleotide and amino acid levels, providing high precision for evolutionary and structural analyses.

• Seamless Containerization & Web Services: Projects can be rapidly developed offline and published as part of web services or microservices architectures, benefiting from GLUE's containerization support for ease of deployment and reproducibility.

• Collaborative Project Management: Hosting GLUE projects in online version control systems (such as GitHub) enables decentralized project development, allowing teams to work independently and merge data or analysis workflows when necessary.

• Integrated Phylogenetics & Sequence Analysis: Phylogenetic tree generation, sequence variation analyses, and metadata-driven querying provide powerful tools for evolutionary and epidemiological investigations, supported by standardized and custom datasets.

To get started, you’ll need to install GLUE. There are two installation options available:

1. Docker-based installation – A convenient and portable setup that simplifies dependencies and ensures compatibility.

2. Native installation – A direct installation on your system, offering flexibility but requiring manual configuration of dependencies.