Add feature for varying substitution rates in MCMC_SEQ

MCMC_SEQ with "-murate" to allow enabling DEO to sample substitution rates across loci.

Fix MCMC_BiMarkers output

• First release using ant build system
• For MCMC_BiMarkers specifically:
  (1) Enable printing likelihood when "truenet" is supplied
  (2) Do not run an MCMC chain if chain length is set to 0
  (3) Fix a bug where sequence alignments were displayed incorrectly if length < 20, and the program crashed if length < 10