EvolveAGene 3: A DNA coding sequence evolution simulation program

Barry Hall

doi:10.1038/npre.2007.1230.1

Abstract

AbstractEvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions and deletions. Output includes a log file, the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments.

Highlights

A variety of methods and computer programs to implement those methods exist for the purpose of reconstructing evolutionary histories from molecular sequence data
Those methods are designed to reconstruct phylogenetic trees, ancestral sequences of common ancestors at the nodes of those trees, and to tease out aspects of adaptive evolution -both positive and purifying selection - along the branches of those trees. All of those methods depend upon data in the form of multiple alignments of the molecular sequences, and a variety of programs exist to estimate those multiple alignments
The problems of multiple alignment and phylogenetic reconstruction are very intertwined; phylogenetic reconstruction depends on correct multiple alignments and multiple alignment reconstruction depends upon correct phylogenetic reconstruction

Summary

Introduction

A variety of methods and computer programs to implement those methods exist for the purpose of reconstructing evolutionary histories from molecular sequence data. When simulated data does not include insertions and deletions there is no need to align the sequences, eliminating an important step that contributes significantly to topological errors in phylogenetic trees.

Results

Conclusion