Next Article in Journal
High Frequency of Either Altered Pre-Core Start Codon or Weakened Kozak Sequence in the Core Promoter Region in Hepatitis B Virus A1 Strains from Rwanda
Next Article in Special Issue
Going Deeper into High and Low Phylogenetic Relationships of Protura
Previous Article in Journal
Transcriptome Profiling and Molecular Therapeutic Advances in Cystic Fibrosis: Recent Insights
Previous Article in Special Issue
Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians
Article Menu
Issue 3 (March) cover image

Export Article

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
Author to whom correspondence should be addressed.
Genes 2019, 10(3), 181;
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)
PDF [2177 KB, uploaded 26 February 2019]


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

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material


Share & Cite This Article

MDPI and ACS Style

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.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top