/ 
SmotifCS-0.07
River stage zero No dependents
/ PhylipParser

NAME

PhylipParser

VERSION

Version 0.05

SYNOPSIS

This module parses phylip output to generate the clusters

use PhylipParser;

PhylipParser::findClusters($treeFile, $matrixFile, $threshold);

EXPORT

SUBROUTINES

findClusters readTree getFinalNodes findSubtree withinSphere getDistance getResNumber

findClusters

Takes a file with the output of kitsch or neighbor (a tree, this is automatically called "outfile" by Phylip) and the distance file used as input to make the tree. Outputs clusters of leaves that lie within the supplied threshold distance. usage: findClusters <dendogram file, output of kitsch or neighbor> >distance file, input to kitsch or neighbor> <threshold distance>

readTree

Subroutine to read phylip tree output

getFinalNodes

findSubtree

Subroutine to find the Subtree

withinSphere

getDistance

getResNumber

AUTHOR

Fiserlab Members , <andras at fiserlab.org>

BUGS

Please report any bugs or feature requests to bug-. at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=.. 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 PhylipParser

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2015 Fiserlab Members .

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.