This Python project investigates the effect population structure has on organisms with smooth or rugged adaptive landscapes. Various sequence to fitness mappings will be explored including:
- RNA secondary structure
- Simple Integer Model
- Bitstrings
- Kauffman's N-K Model
- git://github.com/jaredc-s/structure_and_landscapes.git
- git://github.com/jhmarcus/structure_and_landscapes.git
- git://github.com/nahumj/structure_and_landscapes.git
- Python 2.7
- Ned Batchelder's coverage.py
- Nose
- Pep8
- Numpy
- Matplotlib
1)github: https://github.com/jhmarcus/structure-and-landscapes 2)downloads https://github.com/jhmarcus/structure-and-landscapes/downloads 3)download as zip using the defult archive manager 4)sudo apt-get install python2.7-dev
- version python2.7-dev (2.7.3-0ubuntu3)
- 5)sudo apt-get install build-essential
- version build-essential (11.5ubuntu2)
6)sudo apt-get install pep8 7) pep8 's version (0.6.1-2ubuntu2) 8) sudo apt-get install python-pip 9) pip version (1.0-1build1)
http://www.vrplumber.com/programming/runsnakerun/
depedencies for runsnakerun apt-get install python-profiler python-wxgtk2.8 python-setuptools
http://www.tbi.univie.ac.at/~ivo/RNA/ http://www.tbi.univie.ac.at/~ronny/RNA/vrna2_source.html
follow instructions on install ./configure make sudo make install
version 2.0.7 download source code and use the default archive manager!
Add this line to ~/.bashrc:
export PYTHONPATH=$PYTHONPATH:$PATH_TO_DIRECTORY_CONTAINING_structure_and_landscape