sts-online experiments

This simulation pipeline was used in Effective Online Bayesian Phylogenetics Via Sequential Monte Carlo With Guided Proposals using the following programs.

Program	Version
sts-online	v0.1
MrBayes	v3.2.6
PhyML	v3.2
BAli-Phy	v2.3.8

Requirements

sts-online

The pipeline expects sts-online to be in the PATH.

MrBayes

The pipeline expects mb to be in the PATH.

PhyML

The pipeline expects phyml to be in the PATH.

BAli-Phy package

The pipeline requires the trees-bootstrap program to generate ASDSFs. The pipeline expects trees-bootstrap to be in the PATH.

virtualenv

# install virtualenv if not already installed
pip install virtualenv

# create a virtualenv
virtualenv venv

# activate virtualenv
source venv/bin/activate

# install packages
pip install -r requirements.txt

R packages

# restore packrat project
R --no-restore --slave -e "0" --args --bootstrap-packrat

packrat installs the R packages into the packrat/lib directory.

Bio++ and BppSuite

Running the simulations requires the tools bppseqgen from BppSuite 2.2.0 is required.

On Debian/Ubuntu:

sudo apt-get install bppsuite

If BppSuite isn't available through your package manager, it can be installed from source into the venv prefix, so it'll be in your PATH when the virtualenv is activated:

wget http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz
tar xf bppsuite-2.2.0.tar.gz
cd bppsuite-2.2.0
cmake -DCMAKE_INSTALL_PREFIX=$PWD/../venv
make && make install
cd ..

Running the simulations requires the trees-bootstrap program from the BAli-Phy package

Running the simulations

cd comparison_to_mrbayes
python run_simulations.py

The simulations will probably take several days to complete. Multiple csv files will be produced in the output folder.

Parsing results

cd comparison_to_mrbayes
Rscript --no-restore --slave -e rmarkdown::render("ess.Rmd")

The script will generate the file sts.pdf.