=====
tools
=====

.. automodule:: egglib.tools

---------------------
Specific data formats
---------------------

.. autofunction:: egglib.tools.aln2fas

.. autofunction:: egglib.tools.staden

.. autofunction:: egglib.tools.get_fgenesh

.. autofunction:: egglib.tools.genalys2fasta

.. autoclass:: egglib.tools.Mase
    :members:
    :show-inheritance:

-------------
Data analysis
-------------

.. autofunction:: egglib.tools.LD

---------------------------
Sequence manipulation tools
---------------------------

.. autofunction:: egglib.tools.backalign

.. autofunction:: egglib.tools.concat

.. autofunction:: egglib.tools.longest_orf

.. autofunction:: egglib.tools.rc

.. autofunction:: egglib.tools.translate

.. autofunction:: egglib.tools.ungap

.. autoclass:: egglib.tools.GeneticCodes
    :members:
    :inherited-members:
    :show-inheritance:

-------------------
Sequence comparison
-------------------

.. autofunction:: egglib.tools.compare

.. autofunction:: egglib.tools.motifs

.. autofunction:: egglib.tools.locate

---------------------------------------------
Tools not (directly) related to sequence data
---------------------------------------------

.. autofunction:: egglib.tools.chisquare

.. autofunction:: egglib.tools.correl

.. autofunction:: egglib.tools.ranges

.. autoclass:: egglib.tools.ReadingFrame
    :members:
    :inherited-members:
    :show-inheritance:

.. autoclass:: egglib.tools.Updater
    :members:
    :inherited-members:
    :show-inheritance:
    
.. autofunction:: egglib.tools.wrap