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GpsPrune is a java application to view and manage coordinate data, eg from GPS units. With it you can load a variety of text and Xml formats, view the data (in 2d and 3d), edit and convert the data, correlate photos and audio, create charts and more.
...The GUI plots the GPX track (latitude vs longitude) and lets the user remove GPS points from the beginning and end of the track respectively. There is also a built-in Command Line Interface.
Note: No development anymore since I found out that GpsPrune does all the things I was looking for.