PhyloBayes

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.

Installed version

  • 3.3f (sequential)
  • 1.3f (MPI version)
$ module avail bio/PhyloBayes
 
    bio/PhyloBayes/mpi/1.4f 
    bio/PhyloBayes/seq/3.3f

Load the needed version by module load

Usage

FIXME NEED TO TEST BEFORE FINAL VERSION

Sequential version

mrbayes_seq.sge
#!/bin/bash -l
 
#$ -l h_rt=2:00:0
#$ -o $JOB_NAME.o$JOB_ID
#$ -N job_phylobayes_seq
#$ -V
#$ -pe openmp 3
 
module load bio/PhyloBayes/seq/3.3f
 
pb -d mesDonnes run1&
pb -d mesDonnes run2&
bpcomp -x 100 2 run1 run2

Parallel version

mrbayes_mpi.sge
#!/bin/bash -l
#$ -q normal15d
#$ -V
#$ -N job_phylobayes_mpi
#$ -pe impi_tight 32
#$ -o $JOB_NAME.$JOB_ID.out
 
module load bio/PhyloBayes/mpi/1.4f
 
mpirun -np $NSLOTS pb_mpi -d datafile -cat -gtr chainname

Possible execution schemes

 
mpirun -np <np> pb_mpi -d <datafile> [options] <chainname>
	creates a new chain, sampling from the posterior distribution, conditional on specified data
 
mpirun -np <np> pb_mpi <chainname>
	starts an already existing chain
 
	mpirun -np <np>     : number of parallel processes (should be at least 2)
 
	-cat -dp            : infinite mixture (Dirichlet process) of equilibirium frequency profiles
	-ncat <ncat>        : finite mixture of equilibirium frequency profiles
	-catfix <pr>        : specifying a fixed pre-defined mixture of profiles
 
	-lg                 : Le and Gascuel 2008
	-wag                : Whelan and Goldman 2001
	-jtt                : Jones, Taylor, Thornton 1992
	-gtr                : general time reversible
	-poisson            : Poisson matrix, all relative exchangeabilities equal to 1 (Felsenstein 1981)
 
	-dgam <ncat>        : discrete gamma. ncat = number of categories (4 by default, 1 = uniform rates model)
 
	-dc                 : excludes constant columns
	-t <treefile>       : starts from specified tree
	-T <treefile>       : chain run under fixed, specified tree
 
	-x <every> <until>  : saving frequency, and chain length (until = -1 : forever)
	-f                  : forcing checks
	-s/-S               : -s : save all / -S : save only the trees
 
 
see manual for details

Links