view phylostatistics/tree_support_phyutility.xml @ 0:5b9a38ec4a39 draft default tip

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<tool id="tree_support_phyutility" name="tree_support_phyutility">
	<description>Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees</description>
	<requirements>
		<requirement type="package">phyutility</requirement>
	</requirements>
	<command>
                java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/phyutility.jar -ts -in $treesfile -tree $besttree -out $outtree
	</command>
	<inputs>
		<param format="txt" name="treesfile" type="data" label="Input trees file" help="A file of multiple trees in newick format"/>
		<param format="txt" name="besttree" type="data" label="Target tree" help="Tree to find support for"/>
	</inputs>
	<outputs>
		<data format="txt" name="outtree" label="Support by ${tool.name}" />
	</outputs>
    <help>
**What it does**

Tree support RAxML calculates support values for a given tree using a set of input trees. For example, it can calculate bootstrap support for the ML tree based on a set of trees from a bootstrap analysis.
This is valuable when separating bootstrap analysis from ML analysis, and when separating bootstrap replicates in different runs, which can be concatenated and used as input for this tool.

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**Inputs**

1. Tree file with target tree.

2. Set of phylogenies, branch lengths are ignored.

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**Outputs**

The focal tree is output with support values in Newick tree format.

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**Additional Information**

1. This tool Calls phyutility

2. A similar tool is tree_support_RAxML, which works best with RAxML output

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**Citations**   

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716

    </help>
</tool>