Arlin Stoltzfus


Installation - Bio::NEXUS Installation Instructions.


How to install Bio::NEXUS Perl module.


Bio::NEXUS is packaged as a standard CPAN module, and can be installed using the standard procedures described at and The following sections provide further detail. If you have read and followed the instructions, but still cannot install the software successfully, contact the authors with a precise description of any error messages and of the operating system you are using.

UN*X Installation Notes

Standard UN*X method from the compressed tar file

The standard procedure for installation is to first uncompress the tar-zipped version of the library in a chosen directory and then perform the standard installation sequence below.

        $ cd Bio-NEXUS<version> 
        $ perl Makefile.PL  
        $ make
        $ make test
        $ make install

The final command requires root permission, because by default the "make" script will perform a system-level installation. For a local installation in a user-specified directory, do:

    $ make clean
    $ perl PREFIX=path/to/user/specified/directory

and continue with make, make test, and make install as above.

Automated UN*X installation using CPAN

The alternative way to install Bio::NEXUS library is directly from CPAN using the the following command:

        $ perl -MCPAN -e 'install Bio::NEXUS'

You should have root access for installing the module.

Mac OS X Installation Notes

    Follow the UN*X instructions given above. If you have "admin" privileges on your Mac, then you can do a system-level install by issuing the following instead of just "make install":

        $ sudo make install 

    The system will prompt you for your login password. If you do not have "admin" privileges on your Mac, then you must do a local install as described above for UN*X systems.

Windows Installation Notes

Standard method from the tar-zipped file

After you uncompress the distribution file, the procedure is probably this:

          perl Makefile.PL
          nmake test
          nmake install

You may need to use WinZip (sharware) to decompress and unpack the content of the module.

You may need to download a copy of Microsoft's nmake program from

If you are not familiar with installing modules, or have trouble doing so,you may want to use the alternative method instead (next section) or read the help from the ActiveState page --

Windoze ActivePerl

Windoze users with ActivePerl can take advantage of the Perl Package Manager (PPM), a utility that allows you to install modules, including modules that contain binary extensions. You should consider using PPM to install a module, as this greatly simplifies the management of modules. The commands for installation of Bio-NEXUS library would be.

            $ ppm
  ppm prompt> install Bio-NEXUS 

Additional directions for using PPM are available at


Documentation of Bio::NEXUS is contained in .pod format, either in the docs directory of the distribution or appended to the scripts. Reading the user manual and the brief tutorial should help you use the module effectively for phylogenetics. The tutorial can be read interactively with perldoc, for example

  cd docs
  perldoc Tutorial.pod

or else an html version can be made with pod2html:

  pod2html Tutorial.pod > Tutorial.html

There is also a user manual that is rather incomplete but may be useful in some respects:

  pod2html UserManual.pod > UserManual.html

After installation, the installation directory of files may be deleted.


Tutorial and Bio::NEXUS


Tom Hladish

Arlin stoltzfus