Building trees with SKA
Help 4 / 7
Producing the SNP alignment

The SNP alignment can be extracted from the .skf file produced in the previous step by running

ska align --min-freq 1 --filter no-filter -o output/ska_alignment.aln output/ska_index.skf

which will again take a bit (~2 min) to run. In the above command, the --min-freq option sets the maximum number of missing sites in the alignment to 1 and the --filter no-filter option specifies that no extra filtering should be performed.

Other options include filtering all constant sites with --filter no-const or all constant and ambiguous sites with --filter no-ambig-or-const. Using the last option is equivalent to treating any ambiguous site as an N.

← Previous Next →