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

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 re

SUBMITTER: Yuan F 

PROVIDER: S-EPMC6471834 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature