corresponding changes in order to implement the pair contact model including using jama library to do eigen decomposition and revise gradle file
add PairProteinModel main function
Merge branch 'PairContactModel'

Conflicts:
	build.gradle
	src/main/java/conifer/PairProteinModel.java
	src/main/java/conifer/SimplePhyloModel.java
	src/main/java/conifer/ctmc/EigenCTMC.java