1. updated the manual
2. commented and improved some of Kassians code for TC/IC on partial gene trees
3. Integrated the optimization of the DNA+GAMMA models, that is, unecessary precalculations
   of the P-Matrix are omitted using Andre's approach (yields between 3-5%, performance benefits on smaller partitions
   will be larger)
4. Added three new options:
   --mesquite to print outputfiles for interacting with mesquite
   --silent to avoid printing out info about identical sequences and fully undetermined patterns in the MSA
   --no-seq-check deactivates checking of the MSA for duplicate seqs and undetermined patterns, may save quite
     some time because the run time for this is O(n^2 + m^2) where n is the number of taxa and m the number of patterns
5. Changed command line parsing back to the FNU function that can now also accept long options like --mesquite etc.