Example of diversity analysis implemented in Python using egglib-py. This script imports 100 FASTA-formatted alignments, performs a basic diversity analysis and finally compares the average Tajima's D statistic to a number of neutral coalescent simulations under the standard model. Lines 16, 19, and 44-46 are commented in the text. All operations are performed using the Align class and the simul module of egglib-py (full documentation is included in the reference manual available online).
De Mita and Siol BMC Genetics 2012 13:27 doi:10.1186/1471-2156-13-27