cgMLST Tree
How cgMLST profile-based trees are constructed
Last updated
How cgMLST profile-based trees are constructed
Last updated
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 .
For details about how cgMLST profiles are constructed in Pathogenwatch see the . A cgMLST profile consists of a list of gene loci with one allele code or a "gap" assigned to each.
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.
The matrix is then used to create a Neighbour Joining tree using the . The resulting dendogram is mid-point rooted using .
The software can be found at .
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,