Update README.md
Update README.md
Update README.md
Update usage statement and add ability to print posterior table
Merge branch 'master' of github.com:KorfLab/StochHMM

Conflicts:
	README.md
Fix example sequences

Example sequence 3_16Eddy.fa had a copy of the model copied into the file
so it wouldn't work.
Update README.md
Merge branch 'master' of github.com:KorfLab/StochHMM
Add Installation instruction in INSTALL.txt
Fix stochastic posterior bug

Code for calculating posterior wasn't copied from simple trellis to Stochastic
Trellis.
Update usage to reflect current version number
Merge branch 'development'

Conflicts:
	examples/3_16Eddy.fa
	src/StochHMM.cpp
	src/trellis.h
Added initial functionality for Motif scanning and scoring via PWM class.

Will score simple motif, motif with variable length spacer, or motif with
a defined spacer of variable lengths
Moved source files from xcode directory to src for MotifScorer
Adding doxygen documentation to function within pwm source and header