v0.7.0

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 also be imported using Python's import mechanism. It 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

This is a minor release with added ability to manually set base frequencies.

0.6.0

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 also be imported using Python's import mechanism. It 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

This is a minor release with the following changes to the command-line interface: the options -f and --format is now used to specify the output format. The new option --trees-file make it possible to store just the trees used in the simulations.

0.5.0

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 also be imported using Python's import mechanism. It uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.

The code has been tested with Python 2.7 and 3.6.

Source repository: https://github.com/jmenglund/predsim

With this release, simulated data will be written to standard output (stdout) by default and it is no longer possible to name an output file (but output can still be redirected to a file!). The release also includes a refactoring of the command-line interface, and some tests added to the test suite.

0.4.0

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 also be imported using Python's import mechanism. It uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.

The code has been tested with Python 2.7 and 3.6.

Source repository: https://github.com/jmenglund/predsim

This minor release make it possible to output data to the PHYLIP format and fixes a bug in reading the p-file.

0.3.1

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 also be imported using Python's import mechanism. It uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.

The code has been tested with Python 2.7 and 3.6.

Source repository: https://github.com/jmenglund/predsim

This is a patch release with a minor refactoring of the function for reading the p-file.

0.3.0

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 also be imported using Python's import mechanism. It uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.

The code has been tested with Python 2.7 and 3.6.

Source repository: https://github.com/jmenglund/predsim

This is a minor release that make predsim easier to use as a library (i.e. without the command-line interface).

v0.2.1

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 script uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.

The code has been tested with Python 2.7 and 3.6.

Source repository: https://github.com/jmenglund/predsim

This is a patch release with minor fixes to the documentation.

v0.2.0

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 script uses Seq-Gen for simulating the DNA-sequences and builds on the third-party library DendroPy.

The code has been tested with Python 2.7 and 3.6.

Source repository: https://github.com/jmenglund/predsim

This is a minor release that removes dependency on the third-party library pandas.

v0.1.1

predsim is a 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 script uses Seq-Gen for simulating the DNA-sequences and builds on the third-party libraries DendroPy and pandas.

The code has been tested with Python 2.7, 3.3, 3.4 and 3.5.

Source repository: https://github.com/jmenglund/predsim

This is a patch release with some updates to the documentation.

v0.1.0

predsim is a command-line tool for simulating predictive datasets from MrBayes output files. Datasets can be simulated under the GTR+G+I substitution model or any of its nested variants available in MrBayes (JC69, HKY85 etc.). The script uses Seq-Gen for simulating the DNA-sequences and builds on the third-party libraries DendroPy and pandas.

The code has been tested with Python 2.7, 3.3, 3.4 and 3.5.

Source repository: https://github.com/jmenglund/predsim

This is the first release.