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.

2.0

It is recommended to use TRAL with the docker image or install it locally with the easy_setup system.

GPL-2.0

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.

Delucchi, M., Näf, P., Bliven, S., & Anisimova, M. (2021). TRAL 2.0: Tandem Repeat Detection with Circular Profile Hidden Markov Models and Evolutionary Aligner. Frontiers in Bioinformatics, DOI: 10.3389/fbinf.2021.691865

E Schaper, A Korsunsky, J Pecerska, A Messina, R Murri, H Stockinger, S Zoller, I Xenarios, and M Anisimova (2015). TRAL: Tandem Repeat Annotation Library. Bioinformatics. DOI: 10.1093/bioinformatics/btv306