cgMLST Tree

How cgMLST profile-based trees are constructed

About

For some species Pathogenwatch uses the cgMLST profiles generated by the inhouse cgMLST tool to build allele distance-based Neighbour Joining trees for genomes in a collection. The distances correspond to those used in the cgMLST clustering tool.

Method

Profile construction

For details about how cgMLST profiles are constructed in Pathogenwatch see the cgMLST description page. A cgMLST profile consists of a list of gene loci with one allele code or a "gap" assigned to each.

Distance scoring

The distance is calculated by determining the number of differences over the number of positions in common (i.e. not gaps in both) between the two profiles being compared. Each profile is compared against each other to produce a matrix of distance scores.

Tree construction

The matrix is then used to create a Neighbour Joining tree using the FASTME software. The resulting dendogram is mid-point rooted using Biopython.

Code repository

The software can be found at https://github.com/pathogenwatch-oss/cgmlst-tree.

Citations

FASTME

Vincent Lefort, Richard Desper, Olivier Gascuel, FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program, Molecular Biology and Evolution, Volume 32, Issue 10, October 2015, Pages 2798–2800, https://doi.org/10.1093/molbev/msv150