NOTE: This tool requires Java Runtime Environment 1.7 or higher. 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).

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

William Hillary, Song-Han Lin and Chris Upton*

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 1.7. Please see Java Web Start Setup and Java Web Start Tips for help.


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