Base-By-Base statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Multiple nucleotide sequence alignment Pairwise nucleotide sequence alignment chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

Base-By-Base specifications


Unique identifier OMICS_03733
Name Base-By-Base
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained No


Add your version


This tool is not available anymore.

Publications for Base-By-Base

Base-By-Base in publications

PMCID: 5804112
PMID: 29527230
DOI: 10.1155/2017/9073172

[…] algorithm with 1000 bootstrap repetitions using the kimura 2-parameter substitution model in mega 5.0 [–]. the distribution of polymorphic sites in eight prv genomes was inferred using the software base-by-base []., after intranasal infection of the 28-day-old prv-free piglets, all pigs in the challenge group developed high fever beginning at 2 dpi with temperatures 41.9°c–42.5°c. the clinical […]

PMCID: 5390406
PMID: 28407753
DOI: 10.1186/s12864-017-3680-z

[…] viral bioinformatics resource centre ( [], and the further analyses were conducted using the following tools: viral orthologous clusters database for sequence management (vocs) []; base-by-base for genome/gene/protein alignments [, ]; viral genome organizer for genome organization comparisons (vgo) [], and genome annotation transfer utility for annotation (gatu) []., open […]

PMCID: 5203781
PMID: 27678123
DOI: 10.1093/gbe/evw241

[…] genbank accession number no. cp012805., genomic comparisons were done using cgview server (), and genomic islands were compared using geneious 9.0.2 (). multiple dna alignments were done using the base by base software package (). crisprfinder was used to identify crispr regions in j4206 genome (). the core genes of the three s. anginosus strains were analyzed and mapped for metabolic pathways […]

PMCID: 4753418
PMID: 26876644
DOI: 10.1038/srep21256

[…] (nj) and minimum evolution (me) trees, with 1000 bootstrap replications, were also constructed to corroborate with the ml trees. tree explorer was used for tree visualisation and illustration. base-by-base was used to determine nucleotide and amino acid sequence identity between the different bat mhc genes identified to date., selected bat mhc-i sequence structures were submitted […]

PMCID: 4233057
PMID: 25388670
DOI: 10.1186/s12879-014-0591-3

[…] snp differences between a cultured sample, which was processed with and without whole-genome enrichment, and the c. trachomatis isolate f/sw4 (genbank accession no. nc_017951.1) were called with base-by-base and snps found within coding regions were visualised in a circos-plot [],[]. to assess any potential differences associated with body compartments, non-synonymous snp difference […]

To access a full list of publications, you will need to upgrade to our premium service.

Base-By-Base institution(s)
Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
Base-By-Base funding source(s)
This work was funded by a Canadian NSERC Discovery grant.

Base-By-Base review

star_border star_border star_border star_border star_border
star star star star star

Brynne Gourlay

star_border star_border star_border star_border star_border
star star star star star
I'm using this to compare a few species and so far so good. It has no trouble running on my old and slow computer as well.