estimate_sub_rate

Nucleotide substitution rate estimation workflow

This workflow provides software tools to estimate nucleotide substitution rates over time from multiple sequence alignments using statistical inference. The workflow accompanies the following peer-reviewed journal article:

Julian TR, Baugher JD, Rippinger CM, Pinekenstein R, Kolawole AO, Mehoke TS, Wobus CE, Feldman AB, Pineda FJ, Schwab KJ. Murine norovirus (MNV-1) exposure in vitro to the the purine nucleoside analog Ribavirin increases quasispecies diversity. Virus research. 2016 Jan 4;211:165-173.

Requirements

This workflow has been tested on MACOSX and linux operating systems using recent versions of Perl, R, and X11.

Perl modules:

Bio::fastAPD

R libraries:

optimx

Data for Analysis

A subdirectory named data may be created in the estimate_sub_rate directory to house the data for analysis.

Usage

To run the analysis - From within a shell session, navigate to the estimate_sub_rate directory and type:

bash substitution_transition_analysis.sh ./data

The analysis consists of five steps. The user will be notified when the script has finished. If no errors are reported, the analysis is complete.

Authors

Joseph D. Baugher, Ph.D. and Fernando J. Pineda, Ph.D.
Copyright (c) 2014 Joseph D. Baugher, Ph.D.

Maintainer

Joseph D. Baugher, Ph.D., joebaugher(at)hotmail.com