Code for maxRAF Algorithm

Code for computing the maxRAF, as described in the paper:

Title: Autocatalytic metabolic networks preceded proteins and RNA in evolution
Authors: Joana C. Xavier, Wim Hordijk, Stuart Kauffman, Mike Steel, William F. Martin

Download the code here

File contents:

RAF Algorithm

Instructions:

To run the RAF program:

  1. Save and unzip the file "RAF.zip" in a separate folder.
  2. In a terminal window (in Linux or MacOS) or a command prompt (in Windows), go to the folder where the unzipped files are located (using the "cd" command).
  3. Run these commands:

In Linux or MacOS:

  1. Compile the program by typing "make RAF" on the command line. This will generate an executable file called "RAF".
  2. Run the program by typing "./RAF in.txt" on the command line. This will run the RAF algorithm on the reaction set specified in the input file "in.txt". To run on a different input file, simply specify the name of a different file instead of "in.txt", e.g.,"./RAF myFile.txt".

In Windows:

  1. Run the program by typing "winRAF.exe in.txt" on the command line. This will run the RAF algorithm on the reaction set specified in the input file "in.txt". To run on a different input file, simply specify the name of a different file instead of "in.txt", e.g., "winRAF.exe myFile.txt".

Program output:

The program will print out a list of reaction IDs of those reactions that are in the maxRAF. If the program does not generate any output, there is no maxRAF in the given reaction set. To save the program output into a text file, append "> out.txt" (or any other desired file name) to the command to run the program. For example, "./RAF in.txt > out.txt" (or "winRAF.exe in.txt > out.txt") will run the program on the input file "in.txt" and save the output in the file "out.txt", which can then be used for analysis.