bx-python is a python library and associated set of scripts to allow for rapid
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation