# Unus

A Perl package for phylogenomic analyses

Requirements

Perl modules

• BioPerl, including (at least) bioperl-core and bioperl-run. Be sure you have Muscle or ClustalW (depending on your preference) and BLAST installed. Muscle or ClustalW (or both) are required to be in your PATH. BLAST can be located somewhere else, but you should specify the blastbins option.

• Getopt::Long

• File::Basename

• Pod::Usage

• Log::Log4perl

• Switch

• Parallel::ForkManager

Installation

After installing all the requirements, just locate the Unus libraries in a convenient place. You can specify the location later.

Run

Configuration files

A real example is available at conf/XsPaperBSR_tblastx.conf. Please note that many configuration files at conf/ are required by the example (or any practical file). Therefore, it is usually a good idea to link them from the working directory (wherever you are going to call unus from):

ln -s /path/to/unus/conf/* .

Please see the example for the syntaxis. It is basically a key-value pairs file, supporting # comments. Please note that all values are assumed to be text, even booleans. Therefore, you can not specify a negative boolean (for example tblastx=0 is illegal and can cause Unus to call tblastx). All the booleans are false by default, this means that you can just delete (or comment) boolean options to make them false.

Calling Unus

Option 1: perl oneliner

Ideally, you should use a configuration file. All the parameters can be passed as command-line arguments, but this can result in endless commands. If you already built your configuration file, you can just run:

perl -MUnus::Unus -e 'Unus::Unus->new->run' -- -conf configuration_file.conf

Note that you can also provide a custom location for the Unus library:

perl -I$HOME/my.libs/unus2 -MUnus::Unus -e 'Unus::Unus->new->run' -- -conf configuration_file.conf

You can save this in your ~/.bashrc file as an alias, for example adding the following line:

alias unus2="perl -I$HOME/my.libs/unus2 -MUnus::Unus -e 'Unus::Unus->new->run' --"

And then (after re-loging or running source ~/.bashrc) run:

unus2 -conf configuration_file.conf

Option 2: perl script

As an alternative, you can build a small Perl script like this:

    BEGIN { push @INC, '~/my.libs/unus2' }
    use Unus::Unus;
    my $unus = Unus::Unus->new();
    $unus->run;

And save it somewhere in your $PATH. Mine is located at /usr/local/bin/unus2, but you can also save it, for example, at ~/bin/unus2. Do not forget to give it execution permits:

chmod +x /usr/local/bin/unus2 # Or wherever you saved it.

And then, again, just:

unus2 -conf configuration_file.conf

LICENSE

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.