Close
Help





JOURNAL

Evolutionary Bioinformatics

CMCpy: Genetic Code-Message Coevolution Models in Python

Submit a Paper


Evolutionary Bioinformatics 2013:9 111-125

Technical Advance

Published on 27 Feb 2013

DOI: 10.4137/EBO.S11169


Further metadata provided in PDF



Sign up for email alerts to receive notifications of new articles published in Evolutionary Bioinformatics

Abstract

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/.



Downloads

PDF  (762.65 KB PDF FORMAT)

RIS citation   (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)

Supplementary Files 1   (1.74 KB ZIP FORMAT)

Supplementary Files 2   (4.68 KB ZIP FORMAT)

BibTex citation   (BIBDESK, LATEX)

XML






Quick Links


New article and journal news notification services