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Created with Raphaël 2.2.021Aug116317Jun813May122Jan6Nov2122Dec191312118correct msa read error messagemastermasteradd simple tool to convert numeric MSA to fasta format (only works for 21 AAs)move convertAA to global utilsfix usage message for arma2asciispacing tweakfix bug when restarting runs with ergo check disableduse arma::Col<double> instead of arma::vec for consistenctbump to v0.8.13fix cancellation issue when computing de in mcmcbump to v0.8.11fix bug in computing error of 2p frequency estimatesprint usage when running bmdca_sample without flagsbump to v0.8.10correct note on default value for 'output_binary'create new config flag for saving best stepsrestarting bugfixes:no need to keep passing the model pointertweak name of function for writing positional Dicarry out convergence check in run loop; write steps with low error_totcleanupcompute the root mean squared error of 1p and 2p frequenciesadd functions to compute rel entropy for N and N*Quse dynamic scheduler for correlation loopscompute relative entropy at each positionwrite full final step (helps with restarting)write final step time to run log upon convergencebinarize rel ent grad output and have ascii format match 1p statsclear old code from Graph (should rename this...)bump to v0.8.9clang-format (2)clang-formatfix grave inefficiency in mc sampleruse ARMA_NO_DEBUG rather than .at to disable bounds checks globallyuse dynamic scheduler for two loopsclarify when to use OMP_NUM_THREADSremove superfluous 'weight_given' variableconsolidate MSA constructorsprint msa info immediatelyadd functions to compute hamming distance pairs for an MSAadd notes on .bash_profile on macOS in README