Download ChromoCombine

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ChromoCombine is a tool to help manage the large number of files generated when running ChromoPainter in parallel on a large number of separate compute nodes. You can place all these files into a single directory and ChromoCombine will calculate the correct way to combine them.

It also calculates the effective number of chunks (i.e. the c value).

Basic usage in GUI mode: Press "Add Guide directory" and choose where you put your chromopainter output files. Press "Begin Processing" and you are done! There are some options; see the internal help, and the example.

ChromoCombine for Windows (GUI only)

Windows Installer.
Windows Zip file.
Windows users should use the installer above. An executable version is provided in case you don't have install permissions.

You may also compile from source; you will need wxwidgets, a compiler such as MinGW and (optionally) a build environment such as Code::Blocks.

ChromoCombine for Linux / source (GUI and Command line)

Source code download (Command line and GUI).
Source code download (without GUI).

Dependencies for the command line version:
  • GNU Scientific Library (GSL, development version package libgsl0-dev in Ubuntu, gsl-devel in OpenSUSE)
  • GCC c++ compiler (package build-essential in ubuntu)
Installation Instructions for command line:
tar -xzvf chromocombine-0.0.4GUI.tar.gz # (check
correct version)

cd chromocombine-0.0.4
sudo make install # optional

Dependencies for the GUI:
  • GNU Scientific Library (GSL, development version as above)
  • automake (package automake in Ubuntu and OpenSUSE)
  • wxwidgets 2.8.0+ (packages libwxgtk2.8-dev and wx-common in Ubuntu, wxGTK-devel in OpenSUSE; WARNING: This has many dependencies.)
  • GCC c++ compiler (as above)
Installation Instructions for the GUI:
Assuming that you are continuing from a successful compilation of the command line version:
cd gui
sudo make install # optional
Executables created
  • chromocombine (command line application)
  • gui/chromocombinegui (GUI)
Both executables can be copied into your path, e.g. ~/bin/ . They install to "/usr/local/bin/" by default.

Mac / other (GUI and Command line)

Compilation on the Mac works as for Linux (reported for 10.6, command-line only). Requirements (thanks to John Didion!):
  • MacPorts from
  • GCC: sudo port install gcc46
  • GSL: sudo port install gsl-devel
A current binary is available from Mac Binaries (with compilation notes. Doesn't work for you?). Currently, chromopainter and chromocombine command-line versions are available, with more work required for fineSTRUCTURE and the GUIs.

If you have problems, please let me know at: and I'll do my best to get things working.

Further information

Binaries for Linux can be provided on request but there is no guarantee we will be able to build for your environment.

Note that the software is currently in an early public beta; all problems should be reported, however minor. The ChromoCombine software was written by Dan Lawson. For any queries regarding the software, please contact DL at: