========
wrappers
========

.. automodule:: egglib.wrappers

-----------------------------
Hudson's coalescent simulator
-----------------------------

.. autofunction:: egglib.wrappers.ms

----------------
NCBI BLAST tools
----------------

.. autoclass:: egglib.wrappers.BLAST
    :members:
    :inherited-members:
    :show-inheritance:

.. autoclass:: egglib.wrappers.BL2SEQ
    :members:
    :inherited-members:
    :show-inheritance:

.. autoclass:: egglib.wrappers.BLASTdb
    :members:
    :inherited-members:
    :show-inheritance:

--------------------------
Sequence alignment
--------------------------

.. autofunction:: egglib.wrappers.clustal

.. autofunction:: egglib.wrappers.muscle

--------------------------
Tree building and analysis
--------------------------

.. autofunction:: egglib.wrappers.phyml

.. autofunction:: egglib.wrappers.nj

.. autoclass:: egglib.wrappers.Codeml
    :members:
    :inherited-members:
    :show-inheritance:

----------------
Primer detection
----------------

.. autoclass:: egglib.wrappers.Primer3
    :members:
    :inherited-members:
    :show-inheritance: