The use of orthogonal frequency division multiplexing (OFDM) based underwater acoustic (UWA) modems has raised a growing interest within the scientific community. This is motivated mainly by the relative simple implementation of the OFDM system and its capability to transmit efficiently over long time spread channels. This paper describes the modem developed in the context of COMET project, which aims to produce low cost Autonomous Underwater Vehicles (AUVs) designed to move in an UWA network. This easy configuring software modem is based on a new pulse-shaped OFDM scheme, using the square root raised cosine (RRC) function defined in time domain at both the transmitter and the receiver sides. In addition to its reduced energy consumption, the proposed modem optimizes the spectral efficiency, while neither pilots nor null subcarriers are required with the DPSK modulation use. Flexible and primed to operate with various channel characteristics, it has three different running modes: the standby mode, the locking mode and the decoding mode. To date, the modem is implemented in Matlab language and is real-time running. After the modem presentation in terms of designing modules, we provide supporting results from experiments conducted during sea trials.