1. Supported Graph Structures: JGraphT is a Java library that provides mathematical graph-theory objects and algorithms, allowing users to work with a wide range of graph structures such as directed, undirected, weighted, unweighted, multigraphs, pseudographs, and more. On the other hand, Neo4j is a graph database management system that allows the storage, query, and analysis of large-scale graph data in a distributed and scalable manner. It supports advanced graph structures and properties such as nodes, relationships, properties, labels, and indexes.

2. Query Capabilities: JGraphT provides algorithms and functions for traversing and querying graphs, but it does not offer a dedicated query language or indexing mechanism like Neo4j. Neo4j, on the other hand, supports a flexible and expressive query language called Cypher, which allows users to perform complex graph queries and analysis efficiently. It also provides indexing features to optimize query performance.

3. Storage Model: JGraphT is an in-memory graph library, meaning the graph data is stored in the computer's memory while the program is running. It does not provide persistent storage options by default. In contrast, Neo4j is a disk-based graph database that offers persistent storage of graph data on disk. This allows large-scale graph datasets to be stored and accessed even when the application is not actively running.

4. Fault Tolerance and Scalability: JGraphT is primarily designed for single-machine environments and does not directly support fault tolerance or distributed processing. On the other hand, Neo4j is built for distributed environments and offers features like data replication, clustering, and fault tolerance that enable efficient processing of large-scale graph datasets across multiple machines.

5. Transaction Management: JGraphT does not provide built-in transaction management capabilities. However, it can be used within Java applications that implement their own transaction management mechanisms. Neo4j, on the other hand, provides transactional semantics to ensure data consistency and integrity. It supports ACID (Atomicity, Consistency, Isolation, Durability) transactions and allows users to define and execute complex operations within a single transaction.

6. Community and Ecosystem: JGraphT has an active open-source community and provides ongoing development and support. It offers a range of community-driven resources such as documentation, forums, and sample code. Neo4j also has a thriving community and offers extensive documentation, tutorials, and a range of additional tools and extensions. It has a larger ecosystem built around graph database use cases and provides commercial support options.

In Summary, JGraphT is a Java library for graph-theory objects and algorithms, while Neo4j is a distributed graph database management system. JGraphT focuses on providing graph structures and algorithms for in-memory processing, while Neo4j offers advanced querying capabilities, persistent storage, fault tolerance, scalability, transaction management, and a larger ecosystem for graph data management.