fixed bug in LG4X model
…te an ExaML_modelFile containing the model params of the final tree, I also updated the manual ccordingly.
…ined characters are excluded a priori from the binary file
…nd protein data
2. improved error handling and reporting 3. fixed bug in checkpointing that lead to slightly diverging LnL values for partitions that use a ML estimate of base freqs
…ne arguments used in a restarted run from a checkpoint actually match those from the initial run that generated the checkpoint.
1. the number of unqiue patterns in the alignment 2. the expected memory requirements of ExaML for storing the tip data and the inner Conditional likelihood vectors. Note that, this is slightly different from the on-line memory calculator, since this just computes mem. reqs. for inner CLVs.