view MSA with heatmap

Question

[ivpz]

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.

[ivpz]

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.

[marina.gerges]

I think I want to do exactly what you are mentioning up, did you find answer to your question? thanks in advance

Answer 1

[Alex Reynolds]

You could use lattice or ggplot2 in R to draw dendrograms along an axis of a levelplot (heatmap).