Finding SNPs in a core gene alignment using snp-sites

Today I'm using the snp-sites software (by Page et al 2016) to extract SNPs from core gene alignments (output from Panaroo).

It's really easy to run:
% snp-sites -c -o myout aat.aln.fas

where aat.aln.fas is a core gene alignment (in fasta format) from Panaroo for the gene aat, and 'myout' is the name that I want snp-sites to give to the output file.

It outputs all the sites with SNPs, in fasta format.

The option -c tells snp-sites to only look at alignment columns that have just A/C/G/T characters.

Acknowledgements

Thanks to my colleague Lia Bote for advice on snp-sites.