EcoloPy-UNTBgen

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].

The source is freely available for download here: https://github.com/fransua/ecolopy (Do not hesitate to send us feedback).

Table of Contents:

• Introduction
  • What is EcoloPy?
  • Why an other package?
  • References
• Download and Install
  • GNU/Linux
  • Installing EcoloPy
• Tutorial
  • Just after counting species abundances in an ecosystem
  • Fit to ecological model
  • Comparing Models
  • Generate random distribution
  • Testing for neutrality
  • Saving/Loading Community object
  • References
• Reference Guide
  • Community Class
  • EcologicalModel Class
  • Some utilities
  • UNTB Model Class
  • Ewens Model Class
  • Etienne Model Class
  • Lognormal Model Class

Citation

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