Gene-structure prediction based on spliced alignments of transcript sequences.



PIntron is only distributed as source code.

The latest source code version can be downloaded from the GitHub page as a zip or as tar archive. It is also possible to clone the source repository using the following command:

git clone

We release only stable versions, therefore you are encouraged to always upgrade to the latest version. Anyway, older versions are also available.

Notice that, since version 1.3.0, the JSON schema of PIntron main output file and some of its program options have slightly changed!
The on-line documentation reflects such changes. We encourage all users to migrate to the new (improved) schema, but, if it is not possible, please use version 1.2.59.


PIntron requires the following free software:

  • Python v3.0 or newer. Python v3.1 or newer is recommended
  • Perl (tested on Perl v5.10.1 but it should work also with older versions)
  • A recent version of the standard GNU toolchain (gcc, make).

Compilation and Installation

The build process is driven by the GNU make utility and can be performed by the following invocation:

make dist

The command will produce a compressed archive dist/pintron-*.tar.gz that can be used for the installation or the execution.

The binary package is composed by the directory bin, containing all the executables needed to run PIntron, and the directory doc, containing the documentation and a simple complete example. For installing PIntron, you should copy the executables of the bin/ directory to a directory of the PATH or to a custom directory. If you do not want to mess with your PATH variable or you simply want to test the program, you can invoke PIntron with the complete path of the custom directory and use the --bin-dir program option to specify such directory. For example, if PIntron executables are located in ~/dev/PIntron/bin, then it can be executed with the following commands:

pintron_bindir=~/dev/PIntron/bin ; $pintron_bindir/pintron --bin-dir=$pintron_bindir