Create SNP Tree

The Create SNP Tree tool is inspired by [Kaas et al., 2014].

To generate a SNP tree, first map reads from the individual samples to a common reference and call variants. The corresponding tools are described at:

To create a SNP tree, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Typing and Epidemiology (Image typing_epi_folder_closed_16_h_p) | Create SNP Tree (Image te_snp_tree_16_n_p)

In the first dialog, select reads tracks or read mappings (figure 9.1).

Image createSNP_selectreads
Figure 9.1: Select read mappings to be included in the SNP tree analysis.

Next, select Variant parameters. These determine which SNPs (single-nucleotide polymorphisms) and MNVs (multi-nucleotide variants) to consider for building the SNP tree:

The initial list of SNP positions is reduced based on the above filters. Of the remaining, only variants with relative frequency above 50% (haploid organisms) will be considered. Information about reference and alleles is deduced from the read mappings.

Select the Result metadata table with metadata relevant for your samples. This will allow you to decorate the resulting SNP tree with metadata information, see SNP tree.

Select Tree view settings. (None, K-mer Tree Default, or SNP Tree Default) or your own custom tree setting. Read more on tree settings in general at

In the next dialog, select the tree construction algorithm (figure 9.3).

Image createSNP_treecontructionalgo
Figure 9.3: Choose the tree construction algorithm.

If you selected Maximum Likelihood, the next dialog covers parameters for this algorithm (see figure 9.4). The parameters are described here:

Image createSNP_maxlikelihood
Figure 9.4: Set parameters for maximum likeihood estimation.

In the Result handling dialog, specify the output (figure 9.5).

Image createSNP_resulthandling
Figure 9.5: Create SNP Tree output options.

In addition to the SNP tree, the following are available: