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Under suitable assumptions, the algorithms in [Lin, Tong, Quantum 2020] can estimate the ground state energy and prepare the ground state of a quantum Hamiltonian with near-optimal query complexities. However, this is based on a block encoding input model of the Hamiltonian, whose implementation is known to require a large resource overhead. We develop a tool called quantum eigenvalue transformation of unitary matrices with real polynomials (QET-U), which uses a controlled Hamiltonian evolution as the input model, a single ancilla qubit and no multi-qubit control operations, and is thus suitable for early fault-tolerant quantum devices. This leads to a simple quantum algorithm that outperforms all previous algorithms with a comparable circuit structure for estimating the ground state energy. For a class of quantum spin Hamiltonians, we propose a new method that exploits certain anti-commutation relations and further removes the need of implementing the controlled Hamiltonian evolution. Coupled with Trotter based approximation of the Hamiltonian evolution, the resulting algorithm can be very suitable for early fault-tolerant quantum devices. We demonstrate the performance of the algorithm using IBM Qiskit for the transverse field Ising model. If we are further allowed to use multi-qubit Toffoli gates, we can then implement amplitude amplification and a new binary amplitude estimation algorithm, which increases the circuit depth but decreases the total query complexity. The resulting algorithm saturates the near-optimal complexity for ground state preparation and energy estimating using a constant number of ancilla qubits (no more than 3).