Phylobayes Galaxy Installation and Configuration Instructions

Phylobayes original binaries written by: Lartillot N., Philippe H. Molecular Biology and Evolution

Galaxy and Perl wrapper script written by: Roger Ngo and Todd H. Oakley, UCSB


	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.



Included in this package:

* pb.pl - Perl wrapper script for the Galaxy tool
* pb.xml - Galaxy Phylobayes XML file
* phylobayes_README - Documentation file

Dependencies: PHYLOBAYES 3.3b must be installed on the Galaxy user account.

How to install Phylobayes

1. Ensure phylobayes 3.3b is installed.

2. Modify the $phylobayes_path and $readPB_path to reflect the location
of pb and readpb in your user account. The default is listed below:

my $phylobayes_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/pb';
my $readPB_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/readpb';

3. Copy pb.pl and pb.xml to a folder in the /galaxy-dist/tools directory.

4. Add the XML tool into the tool_conf.xml file in galaxy-dist/

5. Restart Galaxy with:

./run.sh --stop-daemon

and then

./run.sh --reload --daemon