Guides
Building trees with SKA
SKA is a tool for comparing small and highly similar genomes using split k-mers. This guide will explain how to use SKA to build a phylogenetic tree for different Escherichia coli lineages in a few minutes. Although SKA is tailored more towards analysing variation within a lineage, tree-building ends up working fine for the whole species but requires more memory.
Why SKA is good for building phylogenetic trees The basic approach to building a tree with SKA is to generate a SNP alignment using split k-mers and then feed that to a tree building algorithm of choice.
October 18, 2022
A beginner's guide to fitting PopPUNK models
PopPUNK now has a lot of different models available, which can make it hard to know where to start, or to tell if you’ve done the right thing when fitting one to your data.
Some questions I’ll address:
Do you need to fit a new model? Should I subsample my data? Which model should I use? Are my clusters correct? My clusters don’t match MLST/CC tl;dr
Don’t fit a model if you don’t have to.