Abstract We develop a method to deduce the symmetry properties of many-body Hamiltonians when they are prepared in Jordan-Wigner form in which they can act on multi-qubit states. 
Symmetries, such as point-group symmetries in molecules, are apparent in the standard second quantized form of the Hamiltonian.
They are, however,
masked when the Hamiltonian is translated into a Pauli matrix representation required for its operation on qubits.
To reveal these symmetries we prove a general theorem that provides a straightforward method to calculate the transformation of Pauli tensor strings under symmetry operations.
They are a subgroup of the Clifford group transformations and induce a corresponding group representation inside the symplectic matrices.
We finally give a simplified derivation of an affine qubit encoding scheme which allows for the removal of qubits due to Boolean symmetries and thus reduces effort in quantum computations
for many-body systems.
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