Tools
=================
SHEPHARD comes with a collection of tools for working with the various 

Format for function signatures
--------------------------------



Domain tools functions
-------------------------

Domain-associated functions are located in the ``shephard.tools.domain_tools`` module. These tools enable analysis, construction, and manipulation to Domain objects.

.. autofunction:: shephard.tools.domain_tools.domain_overlap
.. autofunction:: shephard.tools.domain_tools.domain_overlap_fraction
.. autofunction:: shephard.tools.domain_tools.domain_overlap_by_position
.. autofunction:: shephard.tools.domain_tools.build_missing_domains
.. autofunction:: shephard.tools.domain_tools.build_domains_from_track_values


Sequence tools functions
--------------------------

Sequence-associated functions are located in the ``shephard.tools.sequence_tools`` module. These tools enable manpulation or search of sequence information.

.. autofunction:: shephard.tools.sequence_tools.build_mega_string
.. autofunction:: shephard.tools.sequence_tools.find_string_positions


Site tools functions
--------------------------

Site-associated functions are located in the ``shephard.tools.site_tools`` module. These tools enable manpulation or search of site information.

.. autofunction:: shephard.tools.site_tools.build_site_density_vector