Question: view MSA with heatmap
0
gravatar for ivpz
4.9 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 • 1.8k views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by ivpz10
1
gravatar for Alex Reynolds
4.9 years ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

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

ADD COMMENTlink written 4.9 years ago by Alex Reynolds27k
0
gravatar for ivpz
4.9 years ago by
ivpz10
United Kingdom
ivpz10 wrote:

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 COMMENTlink written 4.9 years ago by ivpz10
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