predsim is a simple command-line tool for simulating predictive datasets from MrBayes' output files. Datasets can be simulated under the GTR+G+I substitution model or any nested variant available in MrBayes (JC69, HKY85 etc.). The code is contained within a single module that can be imported using Python's import mechanism. The tool uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.
The code has been tested with Python 3.3 and 3.6.
Source repository: https://github.com/jmenglund/predsim
Table of contents
An easy way to get Python working on your computer is to install the free Anaconda distribution.
For most users, the easiest way is probably to install the latest version hosted on PyPI:
$ pip install predsim
The project is hosted at https://github.com/jmenglund/predsim and can also be installed using git:
$ git clone https://github.com/jmenglund/predsim.git $ cd predsim $ python setup.py install
You may consider installing predsim and its required Python packages within a virtual environment in order to avoid cluttering your system's Python path.
$ predsim --help
usage: predsim [-h] [-V] [-l N] [-f #A #C #G #T] [-g N] [-s N] [-n N]
[-o {nexus,phylip}] [-p FILE] [--seeds-file FILE]
[--commands-file FILE] [--trees-file FILE]
pfile tfile
A command-line utility that reads posterior output of MrBayes and simulates
predictive datasets with Seq-Gen.
positional arguments:
pfile path to a MrBayes p-file
tfile path to a MrBayes t-file
optional arguments:
-h, --help show this help message and exit
-V, --version show program's version number and exit
-l N, --length N sequence lenght (default: 1000)
-f #A #C #G #T, --freqs #A #C #G #T
base frequences (overrides any base frequences in
MrBayes' output)
-g N, --gamma-cats N number of gamma rate categories (default: continuous)
-s N, --skip N number of records (trees) to skip at the beginning of
the sample (default: 0)
-n N, --num-records N
number of records (trees) to use in the simulation
-o {nexus,phylip}, --out-format {nexus,phylip}
output format (default: "nexus")
-p FILE, --seqgen-path FILE
path to a Seq-Gen executable (default: "seq-gen")
--seeds-file FILE path to file with seed numbers (e.g. for debugging
purposes)
--commands-file FILE path to output file with commands used by Seq-Gen
--trees-file FILE path to output file with trees used by Seq-Gen
- If base frequences are missing from MrBayes' output, these must be set manually
with the
-f(or--freqs) flag. - It is recommended that you use the
--commands-fileand--trees-fileflags to check the input given to Seq-Gen.
Testing is carried out with pytest:
$ pytest test_predsim.py
Test coverage can be calculated with Coverage.py using the following commands:
$ coverage run -m pytest test_predsim.py $ coverage report -m predsim.py
The code follow style conventions in PEP 8, which can be checked with pycodestyle:
$ pycodestyle predsim.py test_predsim.py setup.py
predsim is distributed under the MIT license.
If you use results produced with this package in a scientific publication, please just mention the package name in the text and cite the Zenodo DOI of this project:
You can select your preferred citation style in the "Cite as" section on the Zenodo page.
predsim relies on other software that also should be cited. Below are suggested citations for Seq-Gen and DendroPy:
- Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235–238. DOI: 10.1093/bioinformatics/13.3.235
- Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26:1569–1571. DOI: 10.1093/bioinformatics/btq228
Markus Englund, orcid.org/0000-0003-1688-7112