The BiVeS Framework is probably the resource you want to use in your project. It is executable from command line (it contains a Main) and combines all /BiVeS modules (see right hand side dependency graph):
All these modules utilize the xmlutils project, which provides advanced features for handling XML trees.
Include the BiVeS Framework via Maven:
<dependency> <groupId>de.uni-rostock.sbi</groupId> <artifactId>BiVeS</artifactId> <version>$VERSION</version> </dependency>