The document provides a comprehensive guide to the software package AUTO 2000, which is used for continuation and bifurcation analysis of ordinary differential equations (ODEs) and partial differential equations (PDEs). The software includes the HomCont algorithms for bifurcation analysis of homoclinic orbits. The manual covers installation, capabilities, running instructions, and detailed descriptions of the command-line user interface (CLUI) and graphical user interface (GUI). It also includes tutorials, demos, and references to related algorithms and documentation. The CLUI is based on the Python scripting language and allows for interactive creation and editing of equations and constants files, as well as advanced programming capabilities. The manual provides examples and detailed explanations of how to use the CLUI to perform various calculations, including bifurcation analysis, solution continuation, and plotting.The document provides a comprehensive guide to the software package AUTO 2000, which is used for continuation and bifurcation analysis of ordinary differential equations (ODEs) and partial differential equations (PDEs). The software includes the HomCont algorithms for bifurcation analysis of homoclinic orbits. The manual covers installation, capabilities, running instructions, and detailed descriptions of the command-line user interface (CLUI) and graphical user interface (GUI). It also includes tutorials, demos, and references to related algorithms and documentation. The CLUI is based on the Python scripting language and allows for interactive creation and editing of equations and constants files, as well as advanced programming capabilities. The manual provides examples and detailed explanations of how to use the CLUI to perform various calculations, including bifurcation analysis, solution continuation, and plotting.