Felipe da Veiga Leprevost > Bio-Tools-Alignment-Overview-0.36 > Bio::Tools::Alignment::Overview

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Module Version: 0.36   Source  

Name ^

Bio::Tools::Alignment::Overview - just another represetation for biological sequence alignment.

Description ^

This module creates a simple and resumed representation of a biological sequence alignment. For now you can ajust the sequence color, with time new customizations will be implemented. If you find any problem please let me know.

Basic Usage ^

instantiate the overview object.

        use warnings;
        use strict;
        use Bio::Tools::Alignment::Overview();

        my $view = Bio::Tools::Alignment::Overview->new();

and pass the required parameters.

        $view->input('path_to_my_align_file');
        $view->outup('path_to_my_output_file'); # no extension is required.
        $view->color('color_name'); # 'red'

create the image.

        $view->make_image();

Methods ^

For the moment the only customization available is the color for the sequences.

Input
        $object->input();

The module is compatible with alignments generated by other programs like ClustalW, MUSCLE and T-COFEE.

Output
        $object->output();

No extension is required for the output file, the module generates automatically a .png file.

Color
        $object->color();

The module depends on GD::Simple for making the images files so the available colors are listed in GD::Simple. The default color is blue.

Make_image
        $object->make_image();

This is the method responsible for generating the image file with png extension.

Author ^

Leprevost, <leprevostfv at gmail.com>

How to cite this work ^

Please refer to the following DOI in order to cite this module.

Bugs ^

Please report any bugs or feature requests to bug-bio-tools-alignment-overview at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Tools-Alignment-Overview. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

Support ^

You can find documentation for this module with the perldoc command.

    perldoc Bio::Tools::Alignment::Overview

You can also look for information at:

License and Copyright ^

Copyright 2012 Leprevost.

This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.

See Also ^

GD::Simple

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