Original Code Import
Add CMake and README.md
Update README.md
Update README.md
Added missing header
Merge branch 'master' of github.com:spond/TN93
Added the 2-file pairwise comparison mode
Compilation error fixes for CentOS
fixed an UNnecessary pairwise distance matrix allocation for the COUNTING mode
Added the minimum overlap command line option
Moved blocking command oustide the main OpenMP loop to speed execution
Resampling tweaks
Added numeric CSV output
Added - options for stdin and stdout
Added GAPMM (AVERAGED and gap vs a character is like an N versus a character) resolution mode
Shortest Path Added (pass 1)
Shortest Path Added (pass 1)
Real valued vectors and better scaling functions
Added two output options (FASTA and JSON)
Added the option to set the source sequence