diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 306f2b3..4543e93 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,15 @@ Changelog ========= +v0.1.1 +------ + +* Updates to the documentation in *README.rst* + +Release date: 2016-08-11 + +`View commits `_ + v0.1.0 ------ diff --git a/README.rst b/README.rst index 4b36111..f143d64 100644 --- a/README.rst +++ b/README.rst @@ -1,13 +1,13 @@ predsim ======= -|Build-Status| |License| +|Build-Status| |PyPI-Status| |License| |DOI-URI| ``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 +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 `_. @@ -86,11 +86,12 @@ Usage -p FILE, --seqgen-path FILE path to a Seq-Gen executable (default: "seq-gen") -It is strongly recommended that you use the ``-c FILE`` option to check the -commands run by Seq-Gen. -Depending on your Python version, you might need to specify the full path to -your Seq-Gen executable with the ``-p FILE`` option. +* It is strongly recommended that you use the ``-c FILE`` option to check the + commands run by Seq-Gen. + +* Depending on your Python version, you might need to specify the full path to + your Seq-Gen executable with the ``-p FILE`` option. Running tests @@ -112,37 +113,34 @@ License ``predsim`` is distributed under the `MIT license `_. -.. .. - +Citing +------ + +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: + +|DOI-URI| + +You can select a citation style from the dropdown menu 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, DendroPy and pandas, +respectively: + +* 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. + +* Sukumaran J, Holder MT. 2010. DendroPy: a Python library for + phylogenetic computing. Bioinformatics 26:1569–1571. + +* McKinney W. 2010. Data structures for statistical computing in python. + *In* Proceedings of the 9th Python in Science Conference + (van der Walt S, Millman J, editors), pages 51–56. + Author ------ @@ -151,5 +149,9 @@ Markus Englund, `orcid.org/0000-0003-1688-7112