I found the augur frequencies subcommand. Can you help me understand how it works?
Say I want to know the frequency changes over time for a particular amino acid mutation. I guess I would need to provide the following parameters?
Possible choices: diffusion, kde // Do you have a description for each of the methods?
–alignments // is genome alignment okay for amino acid frequency? If not, can I run frequencies after running augur translate? What are the output files of augur translate? Can they be input to augur frequencies?
Hi @yzhang2168, thank you for asking about this. We don’t have any documentation for the augur frequencies command yet. This is clearly a major omission and I’ve created an issue on GitHub for us to address this.
The “diffusion” method is described in the supplementary material of Lee et al. 2018 on lines 44-66. The “KDE” method is described in the methods of the Huddleston et al. preprint on lines 568-577 (the “Frequency estimation” subsection). You may also be interested in the source code for these methods, although this is not a replacement for proper documentation.