<tool id="prottest" name="ProtTest 2.4" version="1.0">
	<description>Selection of best-fit models of protein evolution.</description>
	<requirements>
		  <requirement type="package">prottest</requirement>
	</requirements>
	<command interpreter="perl">
		prottest_wrapper.pl -i $input -o $output
	</command>
	<inputs>
	<param name="input" format="phylip" type="data" label="Input alignment (phylip recommended)"/>
	</inputs>
	<outputs>
		<data format="txt" name="output"/>
	</outputs>
	<tests>
	</tests>
	<help>
**What it does**

ProtTest is a bioinformatic tool for the selection of the most appropriate model of protein evolution (among the set of candidate models) for the data at hand. ProtTest makes this selection by finding the model with the smallest Akaike Information Criterion (AIC) or Bayesian Information Criterion (BIC) score. At the same time, ProtTest obtains model-averaged estimates of different parameters (Posada and Buckley 2004) and calculates the importance of each of these parameters. ProtTest differs from its nucleotide homolog Modeltest (Posada and Crandall 1998) in that it does not include likelihood ratio tests (many models implemented in ProtTest are not nested).
	
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**Inputs**

Phylip recommended

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**Outputs**

Text file

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**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu 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

ProtTest 2.4 link: http://darwin.uvigo.es/software/prottest.html

Citation:
Abascal F, Zardoya R, Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics: 21(9):2104-2105.
	</help>
</tool>