A tool to generate distance matrix and sorted species relations from the given minimal or relative absent words.

Download/clone the repository and set root directory as the current directory.

g++ -o dm main.cpp Set.cpp Process.cpp -static-libstdc++ -O3 -DNDEBUG

dm takes 4 arguments (or, at least three arguments) namely Absent Word Type, Dissimilarity Index, Source Directory and (optional) Target Directory. If no Target Directory is supplied, Source Directory is assumed to be the Target Directory. You can also find this help by running dm without any argument.

dm <Absent Word Type> <Dissimilarity Index> <Source Directory> [<Target Directory>]

If all the conditions are fulfilled, output files will be generated in the Target Directory.

For Minimal Absent Words:

For Relative Absent Words:

The source directory should contain a SpeciesFull.txt where each line should contain the names of the species (CRLF is not supported right now, so don't use Notepad to edit SpeciesFull.txt. Use Notepad++ on Windows.), and DNA/RNA sequences of the species in the format described below. No description header should be included.

For Minimal Absent Words: The MAW sequence of a species should be contained in the <species name>.maw.txt file, e.g. human.maw.txt.

For Relative Absent Words: The folders should be named after the referenced species name (let's suppose human). Each folder contains files which are to be named after the referenced species name and the species names it was compared to, joined by an underscore and the extension should be .raw.txt, e.g. human_goat.raw.txt.

See the Examples folder for details. (RC = Reverse Complement)

• SpeciesRelation.txt : Contains sorted species relations (Readable)
• SpeciesRelation.json : Contains sorted species relations (Programmable)
• DistanceMatrix.txt : A plain text of Distance Matrix (Programmable & Readable)
• Output.txt : A formatted Distance Matrix to be used with Match7

The Match7 folder contains the modified Match7 file. The only argument that it takes is the directory containing DistanceMatrix.txt and SpeciesFull.txt files.