Abstract
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).
Highlights
Understanding adaptive evolution at the molecular level is a fundamental goal of evolutionary biology [1,2]
We introduce a Python 3 package called ProtParCon that integrates previously available tools as well as new modules to automate the identification of parallel and convergent amino acid replacements without user intervention
Considering only theconnected branchbranches pairs thatnor involve terminal branches, parallel amino (Figure 3) that are neither branches sharing an evolutionary path acid were replacements in total were found for branch pairs, while convergent amino acid replacements examined along 138 unambiguously aligned amino acid sites
Summary
Understanding adaptive evolution at the molecular level is a fundamental goal of evolutionary biology [1,2]. Identifying parallel and convergent amino acid replacements involves multiple steps and multiple computational routines (e.g., multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and sequence simulations). We iterate over every protein site in the alignment and identify all parallel and convergent amino acid replacements in all. In an the Simulated are evolved according the following parameters: ASR stage, andmodel (3) amino acid frequencies and sequence estimated from trimmed alignment. The differences between numbers of observed and expected parallel and convergent replacements for branch pairs of interest are tested during the TEST stage. At any given replacements along amino acid sites for pairs of branches during the IDENTIFY stage. Since it is not possible to infer parallel and convergent amino acid replacements descended from fromthe thesame sameancestor), ancestor),neighboring neighboring replacementsininconnected connectedbranches branches When the observed number is smaller than the expected number, the lower tail probability is given; when the observed number is greater than the expected number, the upper tail probability is given
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
