TreeMos is designed to work on all modern operating systems, but does require some prerequisites, including Perl and Apache.

For Linux, we have tested TreeMos 1.0 using perl 5.8.6, but TreeMos also works with Perl 5.8.8 on Macs and ActiveState Perl 5.10.0 on Windows. All Perl code is cross-platform.

For Apache, we have tested TreeMos 1.0 on Linux, using Apache 1.

Download TreeMos 1.0e for Linux.

Save this file to the folder you want it to be in, and decompress it using the command:

tar -xjf TreeMos_1.0e_Linux.tar.bz2

In a shell, cd to the folder which is extracted, and to install, type:

. install.sh

When installation is finished, your folder should contain the TreeMos software, and the web interface files will be installed in /usr/local/apache. If this setting is incorrect for your system, you can override it in the file 'config' before you execute install.sh. Double-click ReadMe.html for further information and FAQ (troubleshooting).

To run the program from the command line, place your FASTA files in a directory (the 'alignments' subdirectory in the TreeMos directory is designed for this purpose, and is the one used by the web interface). In a shell, cd to the TreeMos directory and type:

perl treemos alignments or whatever directory path contains your FASTA files

To run TreeMos from the web interface, ensure that Apache is configured to allow Perl scripts to run from the cgi-bin directory, start Apache, and open the page http://localhost/cgi-bin/treemos.