WARNING: Several users have reported problems importing files when running Base-By-Base on Linux machines. We are currently working on a solution. In the meantime, please try running BBB on Mac OS or Windows.

NOTE: This tool requires Java Version 8. Download it here: Java Runtime Environment.
Base-By-Base is a whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it is also provides many of the functions of other generic alignment editors.
In addition to visualizing genomes and protein sequences, Base-By-Base allows the user to estimate simple phylogenetic trees, calculate the numbers of conserved and non-conserved sequence positions, and test simple quantitative hypothesis using novel modifications.

Base-By-Base now includes new primer design tool: j-Codehop!
Link to j-Codehop tutorial.

Getting Started

If you’re new to Base-By-Base, click on the launch button (on the right) and use the Quick Start Page to learn the basics (or if you’re like us…  just start clicking!).

The VBRC also provides additional help resources for Base-By-Base:


If you use this resource please cite the relevant papers (publication list):
Shin-Lin Tu, Jeannette P. Staheli, Colum McClay, Kathleen McLeod, Timothy M. Rose and Chris Upton. 2018
Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes. Viruses 2018, 10(11), 637;

Hillary, W., S.H. Lin, and C. Upton. 2011.
Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments, BMC Microbial Informatics and Experimentation, 1:2

Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004.
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.
Papers which have cited Base-by-Base
The Viral Bioinformatics Resource software is published under the GNU General Public License version 3


If your system does not launch Base By Base, it is probably missing Java Runtime Environment 1.8. Please see Java Web Start Setup and Java Web Start Tips for help.