Selection along a gene

You have a test of selection at each codon of a gene: HyPhy's FEL or MEME, a site model from PAML, or a table of your own.

karyon --selection fel.csv -o selection.svg

Above, the evidence at each site, as -log10 of its p-value, and the sites at p ≤ 0.05 as diamonds. Below, its direction: ω, which is dN/dS, above 1 upwards and below 1 downwards. The ruler counts sites from 1, as HyPhy does.

Your table

HyPhy's CSV is read as it is: alpha, beta and p-value, one row per site in order. Any other table names its columns in a header: a site or codon where the rows are not in order from 1, the rates as alpha and beta, dS and dN, or their ratio as omega, and the evidence as a p-value or a posterior. MEME's beta-, beta+ and p+ are drawn as its two rate classes.

Change it

To	Write
A stricter line	--threshold 0.01
A table of posteriors, from FUBAR or a Bayes empirical Bayes	nothing: the header says so, and --threshold 0.95 moves the line
Some of the sites	site:50-200 as the place, before the file

The example file: fel.csv. Every option: karyon help selection, or the command line reference.