view MSA with heatmap
I'm thinking of representing a multiple sequence alignment (aligned with MUSCLE) of about 400 viral genomes with a heatmap, perhaps next to the phylogenetic tree. Any suggestion on how I can do this or if there are already tools out there which I can use? Thank you.
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marina.gerges •
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ivpz •
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ivpz •
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You could use lattice or ggplot2 in R to draw dendrograms along an axis of a levelplot (heatmap).
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I might need a bit more help here. I presume I'll first need to convert the alignment into some sort of a table with conservation scores and I'm stuck here. Not sure how I can calculate the conservation score for each of the 400+ genomes.
I think I want to do exactly what you are mentioning up, did you find answer to your question? thanks in advance