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We present an open-source software package called "Hamiltonian Open Quantum System Toolkit" (HOQST), a collection of tools for the investigation of open quantum system dynamics in Hamiltonian quantum computing, including both quantum annealing and the gate-model of quantum computing. It features the key master equations (MEs) used in the field, suitable for describing the reduced system dynamics of an arbitrary time-dependent Hamiltonian with either weak or strong coupling to infinite-dimensional quantum baths. This includes the Redfield ME, the polaron-transformed Redfield ME, the adiabatic ME, the coarse-grained ME, and the universal Lindblad ME. HOQST also includes the stochastic Schrodinger equation with spin-fluctuators. We present an overview of the theories behind the various MEs and provide examples to illustrate typical workflows in HOQST. We present an example that shows that HOQST can provide order of magnitude speedups compared to QuTiP, for problems with time-dependent Hamiltonians. The package is ready to be deployed on high-performance computing (HPC) clusters and is aimed at providing reliable open-system analysis tools for noisy intermediate-scale quantum (NISQ) devices. The HOQST Github repository (https://github.com/USCqserver/OpenQuantumTools.jl) provides the starting point for users. Detailed information can be found in the README file.