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<?xml version="1.0"?>
<tool_dependency>
    <package name="noisy" version="1.5.12">
        <install version="1.0">
            <actions>
				<action type="download_by_url">http://www.bioinf.uni-leipzig.de/Software/noisy/Noisy-1.5.12.tar.gz</action>
                <!-- fixes reported bug, remove space introduced after '>' in fasta header output -->
                <action type="shell_command">sed -i 's/\"> \"/\">\"/g' FileFormats.cpp</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>			                
                <action type="set_environment">
                    <environment_variable name="NOISY_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Noisy - identify homo-plastic characters in multiple sequence alignments
Description

In a first phase the rows of the input multiple sequence alignment (MSA) in multi fasta format are reordered to conform to a circular ordering. For this purpose noisy includes the corresponding subset of routines from David Bryant and Vincent Moulton's NeighborNet and Stefan Grünewald's QNet packages. Subsequently, a reliability score for each column of the reordered MSA is calculated. Essentially, the number of character state alterations in an alignment column is counted and compared to the observed count in random shufflings of the column. The uniform pseudo-random number generator Mersenne Twister is used to generate the random shufflings of alignment columns.

Noisy exports a PostScript file, visualizing the quality of the columns of the reordered input MSA, the reliability score of all columns of the reordered input MSA as xy-data and a modified alignment in which columns with a reliability smaller then a cutoff value (set via option --cutoff) are removed. The program noisy is written in ISO C++.
Man Page
Take a look at Noisy's man page.

source code of program  Noisy  release 1.5.12

If you use the program Noisy in your work please cite:
Andreas W. M.Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
Noisy: identification of problematic columns in multiple sequence alignments.
Algorithms Mol Biol, 3:7 (2008).
doi:10.1186/1748-7188-3-7

Stefan Grünewald, Kristoffer Forslund, Andreas W. M.Dress, Vincent Moulton
QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets.
Mol Biol Evol, 24(2):532-538 (2007).
doi:10.1093/molbev/msl180

David Bryant, Vincent Moulton
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
Mol Biol Evol, 21(2):255-265 (2004). doi:10.1093/molbev/msh018s
        </readme>
    </package>
</tool_dependency>