Hello everyone, please is their anyone who can work me through the processes of generating maps using Generic Mapping Tool software, subtract one map from the other and extract values (XYZ) along defined profile?
You can perform all those tasks using QGIS, there are a lot of tutorials on YouTube about this free software.
For example, you can subtract one map from other using the raster calculator (when you are working with raster) or if you are working with vector data, you should use one of the available tools in the QGIS' processing tool box.
For the extraction the (XYZ) values, you should use the Plugin Terrain Profile. It's easy and the results are very useful.
If you are using GMT that means you need specific requirements over your data and type of process that some of GIS packages cannot perform. GMT is line command and script oriented system and for this kind of software you need to learn what each command do. The best way for learning a program like GMT is to follow any tutorial
There are another way to perform maps in the GMT style but I am afraid it seems not well developed yet. That is the python version of GMT:
https://github.com/GenericMappingTools/pygmt
The advantage of chossing python version of GMT is you start to learn also a programming language that can open you to a broad amount of tools posibilities like acces to R libraries, databases, numerical processing and also GIS.