The tree is created using UPGMA and distances shown are computed based on pairwise allelic differences (hamming distance). Missing genes are not included in the count.
The ambition with 1928’s outbreak analyses is to reproduce results from scientific studies and highlight the quality of the results generated by the 1928 platform.
In order to demonstrate the accuracy of outbreak analysis with the 1928 platform, a phylogenetic tree is created from an outbreak of Serratia marcescens. The tree shown in the figure above is generated using the 1928 analysis platform.
In this analysis, 1928 reproduces results from the scientific paper Epidemiological Typing of Serratia marcescens Isolates by Whole-Genome Multilocus Sequence Typing (pmid: 30728192) by John W. A. Rossen, Jill Dombrecht, Diederik Vanfleteren, Katrien De Bruyne, Alex van Belkum, Sigrid Rosema, Mariette Lokate, Erik Bathoorn, Sandra Reuter, Hajo Grundmann, Julia Ertel, Paul G. Higgins, Harald Seifert.
The 1928 Serratia marcescens cgMLST scheme is created from 406 reference genomes giving the scheme 2124 core genes. All genes included in the scheme are present in at least 95% of reference genomes.