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Open AccessArticle

ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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Author to whom correspondence should be addressed.
Genes 2019, 10(3), 181; https://doi.org/10.3390/genes10030181
Received: 3 January 2019 / Revised: 19 February 2019 / Accepted: 21 February 2019 / Published: 26 February 2019
(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)
Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present ProtParCon, a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, ProtParCon implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. ProtParCon also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of ProtParCon, including scripts containing user tutorials, the full API reference and documentation are publicly and freely available under an open source MIT License via GitHub. The latest stable release is also available on PyPI (the Python Package Index). View Full-Text
Keywords: bioinformatics pipeline; parallelism; convergence; adaptation bioinformatics pipeline; parallelism; convergence; adaptation
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Yuan, F.; Nguyen, H.; Graur, D. ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements. Genes 2019, 10, 181.

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