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Hyphy

Hyphy (HYpothesis testing using PHYlogenies) is a package for comparative genetic sequence analysis using stochastic evolutionary models. It performs maximum likelihood phylogenetic analyses of genetic sequence data and supports parallel computing via MPI.

Hyphy is available as a module on Apocrita.

Usage

To run the latest installed version of Hyphy, simply load the hyphy module:

$ module load hyphy
$ HYPHYMP --help
usage: HYPHYMP or HYPHYMPI [-h] [-c] [-d] [-p] [BASEPATH=directory path] [CPU=integer]
[LIBPATH=library path] [USEPATH=library path]
[path to hyphy batch file [analysis arguments]]

For full usage documentation, run HYPHYMP --help.

Example jobs

Serial job

Here is an example job running on 1 core and 1GB memory:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=6:0:0
#$ -l h_vmem=1G

module load hyphy

# The absolute path is required to the template file
# (RELAX.bf) in the example below.
wd=$(pwd)

# As HyPhy is an interactive only application, the echo statements
# below are menu options, initially obtained by walking through the
# interactive menu.
(echo 1; echo ${wd}/example.phy; echo ${wd}/example.tre; echo 1; echo 1; echo 2;) \
  | HYPHYMP ${HYPHY_TEMPLATES_DIR}/SelectionAnalyses/RELAX.bf

Parallel job

Here is an example job running on 2 entire nxv nodes:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe parallel 64
#$ -l infiniband=nxv
#$ -l h_rt=1:0:0

module load hyphy

# The absolute path is required to the template file
# (RELAX.bf) in the example below.
wd=$(pwd)

# As HyPhy is an interactive only application, the echo statements
# below are menu options, initially obtained by walking through the
# interactive menu.
(echo 1; echo ${wd}/example.phy; echo ${wd}/example.tre; echo 1; echo 1; echo 2;) \
  | HYPHYMPI ${HYPHY_TEMPLATES_DIR}/SelectionAnalyses/RELAX.bf

References