<tool id="phylobayes" name="Phylobayes">
	<description>Runs phylobayes</description>
	<command interpreter="perl">pb.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>
	Phylobayes - Bayesian phylogenetic software based on mixture models.
	Lartillot N., Philippe H. Molecular Biology and Evolution. 2004 21(6):1095-1109. 
	
	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/
	
	"A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process."
	http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
	Lartillot N., Philippe H.
	Molecular Biology and Evolution. 2004 21(6):1095-1109.
	
	"Computing Bayes factors using thermodynamic integration."
	http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
	Lartillot N., Philippe H.
	Systematic Biology. 2006 55:195-207.
	
	Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model."
	http://www.atgc-montpellier.fr/download/papers/cat_2007.pdf
	Lartillot N., Brinkmann H., Philippe H.
	BMC Evolutionary Biology. 2007 Feb 8;7 Suppl 1:S4.
	
	"Phylogenomics."
	http://www.atgc-montpellier.fr/download/papers/phylogenomics_2005.pdf
	Philippe H., Delsuc F., Brinkmann H., Lartillot N.
	Annual Review of Ecology, Evolution and Systematics. 2005 36,541-562.

	</help>
</tool>