Removed unused function
Remove unnecessary code
Remove support to simulate sequences from HMM
Replace most rand() usage by <random> equivalents
Make <random> variable naming consistent
Use MCMC::EntropySource::rng for MCMC in plasma
Name the RNG state structs consistently
Remove unneeded code
Ensure identical shuffles are generated with --revcomp
More details on runtime
Fix doc string
Improve runtime reporting
Moving options around
Merge branch 'resources'

Conflicts:
	src/hmm/main.cpp
Removing ruby script for MC based sequence shuffling
Do not try to install the removed script
Fix initialization of transitions from final to initial motif states
Fix plotting of motif logos for inserts and initial/final states
Merge branch 'master' into external_dreme

Conflicts:
	scripts/tikzlogo
	src/plasma/CMakeLists.txt