.. _modules:

Modules
=======

Contents:

Genomics
--------

.. toctree::
   :maxdepth: 1

   modules/AString.rst 
   modules/Blat.rst    
   modules/FastaIterator.rst
   modules/IndexedFasta.rst
   modules/Intervals.rst
   modules/Mali.rst
   modules/MaliIO.rst
   modules/Masker.rst
   modules/SequencePairProperties.rst
   modules/SequenceProperties.rst
   modules/GTF.rst
   modules/Bed.rst
   modules/GO.rst
   modules/GenomicIO.rst
   modules/Genomics.rst
   modules/Maq.rst
   modules/Wiggle.rst
   modules/AGP.rst
   modules/Regions.rst
   modules/Synteny.rst
   modules/AlignedPairs.rst
   modules/ProfileLibrary.rst
   modules/ProfileLibraryCompass.rst

Phylogeny
---------

.. toctree::
   :maxdepth: 1

   modules/Tree.rst
   modules/TreeTools.rst
   modules/RateEstimation.rst
   modules/PamMatrices.rst


Parsers and wrappers
--------------------

.. toctree::
   :maxdepth: 1

   modules/WrapperAdaptiveCAI.rst
   modules/WrapperBaseML.rst
   modules/WrapperBl2Seq.rst
   modules/WrapperBlastZ.rst
   modules/WrapperClustal.rst
   modules/WrapperCodeML.rst
   modules/WrapperDBA.rst
   modules/WrapperDialign.rst
   modules/WrapperENC.rst
   modules/WrapperExonerate.rst
   modules/WrapperGblocks.rst
   modules/WrapperNJTree.rst
   modules/WrapperSlr.rst
   modules/WrapperHmmer.rst
   modules/WrapperMuscle.rst
   modules/WrapperPhylip.rst

Math and Stats
---------------

.. toctree::
   :maxdepth: 1

   modules/CorrespondenceAnalysis.rst
   modules/Histogram.rst
   modules/Histogram2D.rst
   modules/Stats.rst
   modules/MatlabTools.rst
   modules/MatrixTools.rst

Gpipe and OPTIC
---------------

.. toctree::
   :maxdepth: 1

   modules/Exons.rst
   modules/Orthologs.rst
   modules/Prediction.rst
   modules/PredictionFile.rst
   modules/PredictionParser.rst
   modules/Predictor.rst
   modules/BlastAlignments.rst 

Tools
-----

.. toctree::
   :maxdepth: 1

   modules/Experiment.rst
   modules/CSV.rst
   modules/IOTools.rst
   modules/Iterators.rst
   modules/Database.rst
   modules/ExternalList.rst
   modules/ProgressBar.rst

Pipelines
---------

.. toctree::
   :maxdepth: 1

   modules/Pipeline.rst
   pipelinemodules/PipelineTracks.rst
   pipelinemodules/PipelineMapping.rst
   pipelinemodules/PipelineAnnotator.rst
   pipelinemodules/PipelineBiomart.rst
   pipelinemodules/PipelineChipseq.rst
   pipelinemodules/PipelineDatabase.rst
   pipelinemodules/PipelineEnrichment.rst
   pipelinemodules/PipelineGO.rst
   pipelinemodules/PipelineGeneset.rst
   pipelinemodules/PipelineIntervalAnnotation.rst
   pipelinemodules/PipelineKEGG.rst
   pipelinemodules/PipelineLncRNA.rst
   pipelinemodules/PipelineMapping.rst
   pipelinemodules/PipelineMappingQC.rst
   pipelinemodules/PipelineMedip.rst
   pipelinemodules/PipelineMotifs.rst
   pipelinemodules/PipelinePeakcalling.rst
   pipelinemodules/PipelineRnaseq.rst
   pipelinemodules/PipelineTracks.rst
   pipelinemodules/PipelineTransfacMatch.rst
   pipelinemodules/PipelineUCSC.rst
   pipelinemodules/PipelineUtilities.rst

Plotting
--------

   modules/GDLDraw.rst

Other
-----

.. toctree::
   :maxdepth: 2

   modules/RLE.rst
   modules/SVGDuplicationsWheel.rst
   modules/SVGTree.rst
   modules/SVGdraw.rst
   modules/SetTools.rst
   modules/Sockets.rst
   modules/GraphTools.rst
   modules/Cluster.rst

Obsolete
--------

.. toctree::
   :maxdepth: 2

   modules/Intervalls.rst
   modules/IntervallsWeighted.rst
   modules/SaryFasta.rst
   modules/Fasta.rst
   modules/SuffixArray.rst

Unsorted
---------

Modules not sorted into categories.

.. toctree::
   :maxdepth: 2

   modules/Bioprospector.rst
   modules/BlatTest.rst 
   modules/CBioPortal.rst 
   modules/Local.rst
   modules/CSV2DB.rst 
   modules/Expression.rst 
   modules/Fastq.rst 
   modules/GDLDraw.rst 
   modules/Glam2.rst 
   modules/Glam2Scan.rst
   modules/IGV.rst
   modules/IndexedGenome.rst
   modules/Logfile.rst
   modules/MAST.rst
   modules/Motifs.rst
   modules/Tophat.rst
   modules/VCF.rst
   modules/Variants.rst
   modules/WrapperIDR.rst
   modules/WrapperMACS.rst
   modules/WrapperMEDIPS.rst
   modules/WrapperSPP.rst
   modules/WrapperZinba.rst