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<tool id="phylobayes" name="Phylobayes" version="1.0">
	<description>version 3.3b</description>
	<requirements>
		<requirement type="binary">Phylobayes 3.3b</requirement>
	</requirements>
	<command interpreter="perl">
phylobayes33_wrapper.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval
       </command>
	<inputs>
		<param name="filename" type="data" format="txt" label="Input file (ali)" />
		<param name="nchain" type="integer" value="0" label="Number of chains to run" />
		<param name="cycles" type="integer" value="0" label="Cycle interval to run bpcomp and tracecomp" />
		<param name="discrepancies" type="float" value="0.0" label="Discrepancies ceiling" />
		<param name="effectivesize" type="integer" value="0" label="Effective sizes floor"/>
		<param name="burnin" type="integer" value="0" label="Post analysis burnin" />
		<param name="sampleInterval" type="integer" value="0" label="Post analysis sample interval"/>
	</inputs>
	<outputs>
		<data from_work_dir="dataset.con.tre" name="contre" format="txt" />
		<data from_work_dir="dataset.bplist" name="bplist" format="txt" />
	</outputs>
	
	<help>

**How it works**	
PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. 
Compared to other phylogenetic MCMC samplers (e.g. MrBayes ), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. 
It is particularly well suited for large multigene alignments, such as those used in phylogenomics. 

The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests, 
data recoding (analogous to R/Y coding, but for amino-acids), and cross-validation. It also implements a more efficient tree searching MCMC algorithm. 

http://www.atgc-montpellier.fr/phylobayes/

**Citations**
Phylobayes - Bayesian phylogenetic software based on mixture models.

Lartillot N., Philippe H. "A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process." Molecular Biology and Evolution. 2004 21(6):1095-1109.
http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
	
Lartillot N., Philippe H. "Computing Bayes factors using thermodynamic integration." Systematic Biology. 2006 55:195-207.
http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
	
Lartillot N., Brinkmann H., Philippe H. "Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model." BMC Evolutionary Biology. 2007 Feb 8;7 
Suppl 1:S4.
	
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
	</help>
</tool>