GitLab

cm.cpp and mctr.h sped up: In mctr, get_aa(...) replaced wtih 2 static arrays, vector .at() calls replaced by [], increment_bits_it0(...) rewritten with get_score(...) function called only once per sequence.

readme.txt --> README. Deleted commented out code and also code that wasn't necessary for the class's main functions (e.g. all_matches and all_all_matches)

readme.txt updated. Examples directory modified. Output statements from programs reduced. All programs and files not involved in the core SlopeTree routines removed. Some minor code cleanup.

Entropy calculation moved to its own program dentrop.cpp. 3 scripts added: dSTM.sh which runs SlopeTree from the info file generation through to the generation of the distance matrix; and dMT.sh and pFilt.sh which provide intermediate files for filtering procedures.