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Detect and evaluate tandem repeats in genomic sequence data.

Project Description

TRAL is a highly modularized, flexible sequence tandem repeats annotation Python2/3 library.

  • Large scale annotation of tandem repeats with de novo detectors, and sequence profile models
  • Statistical significance testing, overlap detection, and filtering of annotations
  • Refinement of tandem repeat annotations with circular profile hidden Markov models
  • User-defined output formats

The source code is documented on GitHub IO.

Version

0.3.5

Installation

TRAL is available on Pypi and can be installed with pip for Python>=3.2:

$ pip install tral

See also more extensive Installation instructions.

License

GPL

Dependencies

Some of TRAL’s functions depend on external software (Installation instructions for dependencies). This includes creation of sequence profile hidden Markov models, alignment of tandem repeat units, and de novo repeat detection.

Release history Release notifications

This version
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0.3.5

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0.3.4

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0.3.3

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0.3.2

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0.3.1

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0.3.0

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Filename, size & hash SHA256 hash help File type Python version Upload date
tral-0.3.5.tar.gz (324.9 kB) Copy SHA256 hash SHA256 Source None Apr 21, 2015

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