a Python package to test for Unified Neutral Theory of Biodiversity and biogeography in Large dataset. EcoloPy deal with species abundance and diversity data. It allows to fit this data into ecological models and implements some statistical tests. It is able to deal with large dataset like genetic element content of mammalian genomes.

The package was implemented in the context of a study of the distribution of genetic elements in Eukaryotic genomes [Serra2013].

http://fransua.github.io/ecolopy/

Please refer to the following article if you use this package to analyze or process results that are part of a published work:

Serra, F., Becher, V., & Dopazo, H. (2013). Neutral Theory Predicts the Relative Abundance and Diversity of Genetic Elements in a Broad Array of Eukaryotic Genomes. PloS One, 8(6), e63915. doi:10.1371/journal.pone.0063915

This is to install python packages easily.

sudo apt-get install python-setuptools

http://www.mpfr.org/

cd /tmp/
wget http://www.mpfr.org/mpfr-current/mpfr-3.1.2.tar.gz
tar xzvf mpfr-3.1.2.tar.gz
cd mpfr-3.1.2/
./configure
make
make check
sudo make install

http://gmplib.org/

cd /tmp/
wget ftp://ftp.gmplib.org/pub/gmp/gmp-5.1.2.tar.bz2
tar xjvf gmp-5.1.2.tar.bz2
cd gmp-5.1.2/
./configure
make
make check
sudo make install

http://www.multiprecision.org/

cd /tmp/
wget http://www.multiprecision.org/mpc/download/mpc-1.0.1.tar.gz
tar xzvf mpc-1.0.1.tar.gz
cd mpc-1.0.1/
./configure
make
make check
sudo make install

for huge numbers.

sudo apt-get install python2.7-dev libmpfr-dev libgmp3-dev libmpc-dev
sudo easy_install gmpy2

for optimization of log likelihood

sudo easy_install scipy

sudo easy_install numpy

Not compulsory, only to draw graphs

sudo easy_install matplotlib

sudo python setup.py install

test usage:

python test_all.py full

• do something with metacommunity

Broken -> problem with scipy install at travis.