- specification of results folder (will be generated by `snippy`)
Here, we are mostly interested in analysing the samples associated with the outbreak:
Perhaps: Here, we are mostly interested in analysing the samples that we know from cgMLST are associated with the outbreak:
SaH1P10622<br>
SaH1P30922<br>
...
...
@@ -166,7 +166,7 @@
You can find more info on the implemented models here: http://www.iqtree.org/doc/Substitution-Models#dna-models
* Inspect the phylogeny using **Figtree** - download it from here if you have not already done so. You should be able to open the .tre file directly via the SFTP feature of your terminal client.
* Inspect the phylogeny using **Figtree** - download it from https://github.com/rambaut/figtree/releases if you have not already done so. You should be able to open the .tre file directly via the SFTP feature of your terminal client.
* When opening the .tre file, Figtree will ask you to give a label to the node values. These are your bootstrap values. You can choose display them under "Node Labels".
