GEvo

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GEvo - Genome Evolution Analysis
GEvo-logo.png
GEvo Screenshot.png

Typical GEvo Analysis
Software companyCoGe Team
Analysis TypeCompare multiple genomic regions for synteny and other forms of genome evolution
Working stateReleased
Tools Utilizedblastn, tblastx, blastz, CHAOS, LAGAN, DiAlign 2
Websitehttp://synteny.cnr.berkeley.edu/CoGe/GEvo.pl

GEvo is CoGe's Genome Evolution Analysis tool, designed to visually compare genomic regions using both local and global alignment algorithms.


Introduction

The purpose of GEvo is to compare multiple genomic regions from any number of organisms using a variety of different sequence comparison algorithms in order to quickly identify patterns of genome evolution

Alignment Algorithms

Current GEvo can use:

  • BlastZ: DNA-DNA Local Alignment Algorithm. Good for finding large regions of conserved sequence.
  • BlastN: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence.
  • TBlastX: Translated DNA-Translated DNA Local Alignment Algorithm. Good for finding small regions of divergent, but evolutionarily conserved, genomic sequence where protein translated sequence is more conserved than DNA sequence.
  • Chaos: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence. Uses fuzzy matches so it can seed its alignment on small sequences than BlastN. However, it is slower than BlastN.
  • DiAlign: DNA-DNA Global Alignment Algorithm. Global alignment can be seeded using local alignment algorithm. Good for alignment the entire sequence.

GEvo supports using Chaos, BlastN, and BlastZ for seeding DiAlign.

  • Lagan: DNA-DNA Glocal Alignment. Using a hybrid alignment approach.

Overview

We have docs for this

Documentation

You should read this if you are confused.

Tutorials

We has them.

References