Simple Distance Matrix Calculator

This is a simple little script that is a bare-bones distance matrix calcualtor and was written by Norbert Schorghofer, one of my fellow UHNAI postdocs. This script takes as it's input a tab-deliminated text file containing only numbers. The arrangment of the data is so that each colum is a differnet species and each row is a different motif value. The distance matrix is then calculated using the following equation:

The output is a distance matrix of only numbers where each row is a single species. The order of the data is so that the firts colum of the input is the first row of the output and so forth. The output file can then be manipulated in a spreadsheet program to prodcue a distance matrix than can be input into whatever your favorite tree making program is.

Click here to download the distance matix calculator script (a.out).

How to use the script

1) First, prepare your input file in the correct format (numbers, tab deliminated colums, each colum is a species and each row is a motif).

2) Put the input file into the same directory as the a.out script

3) Open a terminal window and change into the directory that has the input file and script.

4) Execute the program by typing: ./a.out inputfilename N where N is the number of Rows

5) The output is written in a file called dmatrix.

That's it. I'm trying to get the computer folks to write a more complicated version of this taht automates making the input files and can compare personalized inputs to a library I am building, so check back for that.