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lucasnell / jackalope

A swift, versatile phylogenomic and high-throughput sequencing simulator
https://jackalope.lucasnell.com
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Parameter order for GTR model #16

Closed adrienlemeur closed 1 year ago

adrienlemeur commented 1 year ago

Hello, I am trying to mutate a fasta sequence using a GTR model, but I can not figure out the abcdef parameter order. The vignette("sub-models") gives an indication but I am not familiar with the notation. I got the A -> T, A -> C, etc. rates with IQtree model finder, it should be good right ? Thanks ~ Adrien

adrienlemeur commented 1 year ago

went with : c(GTR$mut$C_T, GTR$mut$A_T, GTR$mut$G_T, GTR$mut$A_C, GTR$mut$C_G, GTR$mut$A_G) but the resulting substitution rate matrix is not what I expected ?

lucasnell commented 1 year ago

Hi Adrien, The parameter order follows Yang (2006), so the matrix rows and columns are ordered T, C, A, then G. The vignette is not rendering matrices properly on my computer, but the online documentation (link) seems to be rendering okay.

The order you're using looks good. I've never used ModelFinder, but perhaps the difference you're seeing is because the parameters a, b, ...,f get multiplied by the allele frequencies? (The first column get multiplied by $\pi_T$, second by $\pi_C$, etc.)

adrienlemeur commented 1 year ago

Oh thank you very much, indeed the vignette in R studio was rendered as a single line. I have made a mistake when calculating the parameters, but I should be fine now. Thank you very much !