Codon Optimal Likelihood Discoverer

This COLD homepage has the latest version for downloading.


Dowload Version 1.2.2

Installation Instructions

  • Download the package. (You may need to turn off pop-up blocking to download in some browsers.)
  • Unzip the package (It was zipped using Gnu zip)
  • Extract all the files.
  • This will extract a directory "Documentation", which contains files with more detailed instructions.
  • Run "make" in the directory containing the files. (Usually, this just involves typing "make"). You may wish to set some compilation options at this point (in particular, the directory in which you want to install the data files) - see for details. Note that you will need to have a c++ compiler for this step.
  • If it works, you can install the program by typing "make install". This should mean that the program is available to be run from anywhere on your system. Note that the installation directory should be set when running the first make command, as this compiles the correct directories for file-searching into the program. These settings are saved during compliation, and automatically used when you type make install
  • Notes on Installation

    The package has not been extensively tested for portability. The following is a list of tested systems and configurations, with any notes about installation and running.

    Operating SystemCompilerIssues
    Ubuntu Linux 10.04
    Linux Kernel: 2.6.32-27
    64 bit
    Gnu c++ compiler g++
    Version 4.4.3

    No issues with compilation or execution

    Linux Mint 10 Julia
    Linux Kernel: 2.6.35-22-generic
    64 bit
    Gnu c++ compiler g++
    Version 4.4.5

    No issues with compilation or execution

    Centos Linux release 5.5 (Final)
    Linux Kernel: 2.6.18-194.11.4.el5
    64 bit
    Gnu c++ compiler g++
    Version 4.4.0

    No issues with compilation or execution

    Gnu c++ compiler g++

    No issues with compilation or execution

    If you install it successfully, or have difficulty installing it, on a system or configuration not listed here, or if your configuration is listed here, but the results are different, please send me an email ( and I'll update the website. If necessary, I may also update the software to fix any problems.


    The documentation files are all included in the package, in the directory Documentation. However, brief summaries are available here.
    installation.htmlInformation on installing COLD and configuration options.
    cold.htmlInformation on running COLD, command-line options and interpreting the output.
    files.htmlInformation on the format of various files used by COLD.
    utilities.htmlInformation on the utilities provided with COLD to help with setting up files.

    These are quite old, so some things may be out of date. A more detailled and up-to-date manual is here. It is still not completely up-to-date.

    Old versions

  • Version 1.0.0
  • Version 1.1.0
  • Version 1.1.1
  • Version 1.2.0
  • Version 1.2.1