Reorganized code plus Gotoh
added remaining files
ttp
almost working heuristics
some debugging
Almost working heuristics
almost almost working heuristics
working heuristics although not estimating the alpha well
wrong likelihood
problems with nan in likelihood calculation
needs rewriting the gamma likelihood calculation
redone pt matrices, needs more adjustments. Version below is a working
version sans triplet likelihood
Proper triple site patterns
some changes in sampling
Working sampling
Slow estimation
Indel estimation base classes
Working model heuristics
2pass optimization with a bug
minor fixes, viterbi still does not work