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<tool id="JModelTest" name="JModelTest 1.0" version="1.0">
	<description>Statistical selection of best-fit models of nucleotide substitution</description>
	<command interpreter="perl">
		#if $likelihoodInput.likelihoodStyle == "-t":
			jmodeltest.pl $input -t ${likelihoodInput.likelihoodPARAM} $criterion $inputType
		#elif $likelihoodInput.likelihoodStyle == "-u":
			jmodeltest.pl $input -u ${likelihoodInput.likelihoodFILE} $criterion $inputType
		#else:
		#end if#
	</command>
	
	<inputs>
		<param name="inputType" type="select">
			<option value="fasta">FASTA</option>
			<option value="nex">NEXUS</option>
			<option value="phylip">Phylip</option>
		</param>
	
		<param name="input" type="data" label="Input file" help="Can be: PHYLIP, FASTA or NEXUS"/>
		
		<conditional name="likelihoodInput">
			<param name="likelihoodStyle" type="select" label="Likelihood Option" >
				<option value="-t">Base Tree</option>
				<option value="-u">User Specified Tree</option>
			</param>
			
			<when value="-t">
				<param name="likelihoodPARAM" type="select" label="Likelihood options">
					<option value="fixed">Fixed BIONJ-JC</option>
					<option value="BIONJ">BIONJ</option>
					<option value="ML">ML Optimized</option>
				</param>
			</when>
			
			<when value="-u">
				<param name="likelihoodFILE" type="data" format="trees" label="User specified tree file" />
			</when>
		</conditional>

		<param name="criterion" type="select" label="Information criterion">
			<option value="AIC">AIC</option>
			<option value="BIC">BIC</option>
			<option value="DT">DT</option>
			<option value="hLRT">hLRT</option>
		</param>
		
	</inputs>
	
	<outputs>
		<data name="output" from_work_dir="output.txt" format="txt" />
		<data name="errors" from_work_dir="err_log.txt" format="txt" />
	</outputs>
    <help>
**What it does**

"jModelTest is a new program for the statistical selection of models of nucleotide substitution based on “Phyml” (Guindon and Gascuel 2003. 
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.). It implements 5 
different selection strategies, including “hierarchical and dynamical likelihood ratio tests,” the “Akaike information criterion,” the 
“Bayesian information criterion,” and a “decision-theoretic performance-based” approach. This program also calculates the relative 
importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny."

(Posada, 2008; see full citation below)

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**Inputs**

Phylip, FASTA, NEXUS

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**Outputs**

Text file

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**Additional Information**

Please direct questions or comments to [e-mail] or, if you can, enter them on the osiris_phylogenetics site at 
bitbucket.org

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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

jModelTest: Posada, D. 2008. jModelTest: Phylogenetic Model Averaging. Mol Biol Evol 25 (7): 1253-1256.

Phyml: Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood". Systematic 
Biology 52: 696-704.
    </help>
</tool>