Genomics Phylogenomics


A common practice in the analysis of pathogens and their strains is using single nucleotide polymorphisms (SNPs) to reconstruct their evolutionary history. However, genome-wide SNP-based phylogenetic trees are rarely analyzed without any further information. Including the underlying SNP data together with further metadata on the respective samples in the exploration process can facilitate linking genomic and phenotypic properties of the samples. We introduce Evidente, a web-application that provides an interactive visual analysis interface for the simultaneous interrogation of phylogenetic relationships, genome-wide SNP data and metadata for samples of an organism. Besides visualizing the phylogenetic tree, Evidente classifies SNPs as supporting or non-supporting of the tree structures and shows the distribution of both types of SNPs among samples and clades of interest. Furthermore, additional metadata can be included in the visualization. Lastly, Evidente includes an enrichment analysis to identify over-represented genomic features encoded by GO-terms within the clades of the tree.

Visit Evidente here:

For a stand-alone version of Evidente visit our GitHub site:


Evidente has been published in Bioinformatics Advances:

Mathias Witte Paz, Theresa A Harbig, Kay Nieselt, Evidente – A visual analytics tool for data enrichment in SNP-based phylogenetic trees, Bioinformatics Advances, 2022;, vbac075,

Advanced example data

Mycobacterium leprae – From Schuenemann et al (2018, Publication). The study analyzed over 159 samples with 3,124 identified SNP.

Treponema pallidum – From Pla-Díaz et al. (2021, Publication). The study analysed 75 Treponema pallidum samples with a total of 2,550 different SNP positions.