Combine multiple sequence alignment matrix and phylogenetic tree

Question

[Sebastian Obermaier]

Hey guys, Can anybody tell me how to produce figures such as this one in R? I'm assuming one can use a finished MSA and tree for it, but I couldn't find the proper commands.

Thanks!

Edit: so, for those of you that don't see the figure, it's basically just a matrix that shows pairwise identity of a multiple sequence alignment (colored as a heatmap). Next to the matrix, there is a phylogenetic tree, whose taxa are connected to the rows in the matrix.

[Mensur Dlakic]

Edit: so, for those of you that don't see the figure, it's basically just a matrix that shows pairwise identity of a multiple sequence alignment (colored as a heatmap). Next to the matrix, there is a phylogenetic tree, whose taxa are connected to the rows in the matrix.

Even though that's an accurate description, I doubt that anyone would grasp the complexity of this figure from your description alone. What makes you think that some of us don't see the figure?

pyani will do the right-hand portion of this figure, and of course there are numerous programs that can do the left-hand side.

What is the source of this figure? Do they not explain anything about how it was made?

[Sebastian Obermaier]

It's from this publication, which doesn't mention how the figures were created: DOI: 10.3389/fmicb.2019.01758

I got a comment from somebody who wasn't shown the figure, so I tried to describe it. Anyway, so it seems there isn't an out-of-the box solution in R for this?

[Mensur Dlakic]

Although it shouldn't be required because it is on to authors to correctly describe the procedure, sometime we have to be detectives. There is no doubt that the identity matrix in that paper was made using this program:

• https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0108277
• http://web.cbio.uct.ac.za/~brejnev/

Maybe the same software can do the tree on the side, or they added it by hand.