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API Reference
==============

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.. toctree::
   :hidden:

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   hmmer <hmmer>
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   easel <easel>
   plan7 <plan7>
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   daemon <daemon>
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   errors <errors>
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.. currentmodule:: pyhmmer

.. automodule:: pyhmmer


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.. only:: html

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    HMMER
    -----

    .. autosummary::
        :nosignatures:

        pyhmmer.hmmer.hmmsearch
        pyhmmer.hmmer.phmmer
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        pyhmmer.hmmer.nhmmer
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        pyhmmer.hmmer.hmmpress
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        pyhmmer.hmmer.hmmalign
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    Easel
    -----

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    Data Structures
    ^^^^^^^^^^^^^^^

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    .. autosummary::
       :nosignatures:

       pyhmmer.easel.Bitfield
       pyhmmer.easel.KeyHash
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    Sequences
    ^^^^^^^^^

    .. autosummary::
       :nosignatures:

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       pyhmmer.easel.Sequence
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       pyhmmer.easel.TextSequence
       pyhmmer.easel.DigitalSequence
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       pyhmmer.easel.SequenceFile
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    Alignments
    ^^^^^^^^^^

    .. autosummary::
       :nosignatures:

       pyhmmer.easel.MSA
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       pyhmmer.easel.TextMSA
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       pyhmmer.easel.DigitalMSA
       pyhmmer.easel.MSAFile


    Linear Algebra
    ^^^^^^^^^^^^^^

    .. autosummary::
       :nosignatures:

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       pyhmmer.easel.Vector
       pyhmmer.easel.VectorF
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       pyhmmer.easel.VectorU8
       pyhmmer.easel.Matrix
       pyhmmer.easel.MatrixF
       pyhmmer.easel.MatrixU8


    Miscellaneous
    ^^^^^^^^^^^^^

    .. autosummary::
       :nosignatures:

       pyhmmer.easel.Alphabet
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       pyhmmer.easel.Randomness
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       pyhmmer.easel.SSIReader
       pyhmmer.easel.SSIWriter

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    Plan7
    -----

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    Hidden Markov Model
    ^^^^^^^^^^^^^^^^^^^

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    .. autosummary::
        :nosignatures:

        pyhmmer.plan7.HMM
        pyhmmer.plan7.HMMFile
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        pyhmmer.plan7.HMMPressedFile
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    Profile
    ^^^^^^^

    .. autosummary::
        :nosignatures:

        pyhmmer.plan7.Profile
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        pyhmmer.plan7.OptimizedProfile
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        pyhmmer.plan7.Background


    Pipelines
    ^^^^^^^^^

    .. autosummary::
        :nosignatures:

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        pyhmmer.plan7.Pipeline
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        pyhmmer.plan7.LongTargetsPipeline
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        pyhmmer.plan7.Builder


    Results
    ^^^^^^^

    .. autosummary::
        :nosignatures:

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        pyhmmer.plan7.TopHits
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        pyhmmer.plan7.Hit
        pyhmmer.plan7.Domains
        pyhmmer.plan7.Domain
        pyhmmer.plan7.Alignment
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    Traces
    ^^^^^^^

    .. autosummary::
        :nosignatures:

        pyhmmer.plan7.TraceAligner
        pyhmmer.plan7.Traces
        pyhmmer.plan7.Trace


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    Iterative Searches
    ^^^^^^^^^^^^^^^^^^

    .. autosummary::
       :nosignatures:

       pyhmmer.plan7.IterativeSearch
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       pyhmmer.plan7.IterationResult
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    Miscellaneous
    ^^^^^^^^^^^^^

    .. autosummary::
        :nosignatures:

        pyhmmer.plan7.Cutoffs
        pyhmmer.plan7.EvalueParameters
        pyhmmer.plan7.Offsets
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        pyhmmer.plan7.PipelineSearchTargets
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    Daemon
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    ------

    .. autosummary::
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        :nosignatures:
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        pyhmmer.daemon.Client
        pyhmmer.daemon.IterativeSearch
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    Errors
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    ------

    .. autosummary::
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       :nosignatures:
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       pyhmmer.errors.AllocationError
       pyhmmer.errors.UnexpectedError
       pyhmmer.errors.EaselError