Question: view MSA with heatmap
0
gravatar for ivpz
5.9 years ago by
ivpz10
United Kingdom
ivpz10 wrote:

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.

alignment • 2.3k views
ADD COMMENTlink modified 12 months ago by marina.gerges0 • written 5.9 years ago by ivpz10

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.

ADD REPLYlink modified 3 months ago by RamRS26k • written 5.9 years ago by ivpz10

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

ADD REPLYlink written 12 months ago by marina.gerges0
1
gravatar for Alex Reynolds
5.9 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

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

ADD COMMENTlink written 5.9 years ago by Alex Reynolds29k
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