GrapeTree Documentation

GrapeTree is a fully interactive, tree visualization program within EnteroBase, which supports facile manipulations of both tree layout and metadata. It generates GrapeTree figures using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree) similar to PhyloViz, or an improved minimal spanning tree algorithm which we call MSTree V2.

Here are materials to help you use GrapeTree:

About GrapeTree

GrapeTree is named after the clusters of related bacterial strains that tends to be presented in minimal spanning trees. Our GrapeTree GUI is available within EnteroBase once you have created a workspace or connected to somebody else’s workspace. fire It is also available here as a stand-alone version. The integrated EnteroBase version interacts directly with EnteroBase data. The stand alone version calculates trees from character data, visualizes pre-calculated trees and annotates them with information from supplied metadata.

GrapeTree aims to address two central issues:

  • It is difficult to infer clusters from classical phylograms when showing large numbers of taxa.
  • Tree construction methods based on Multi Locus Sequence Type (MLST) data (and extensions such as core genome MLST) do not correctly handle missing alleic information (See MSTreeV2 below).

GrapeTree is easy to integrate into existing web services. Since the release of our source code, Keith Jolley has written a GrapeTree wrapper specific for the BigsDB website/database environment, and thereby enabled GrapeTree functionality for all the databases served by PubMLST.

About MSTreeV2

MSTree V2 is a novel minimum spanning tree which is better suited for handling missing data than are classical MSTrees. First, a directed minimal spanning arborescence (dMST) (Edmond’s algorithm) is calculated from asymmetric (directional) distances with tiebreaking of coequal branches based on allelic distances from a harmonic mean. Local branch recrafting is subsequently performed to eliminate the spurious branches that can arise within minimum spanning trees.

Citation

If you use GrapeTree please cite the preprint:

Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, JA Carrico, M Achtman (2017) “GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens”, bioRxiv 216788; doi: https://doi.org/10.1101/216788