Add bootstrap values to tree branches in anvi'o interactive interface

[ShaiberAlon]

I know this has been raised before by @tdelmont, and I think it justifies an issue. @ozcan, I don't know how complicated this would be for you, but I'm quite certain that this would be a popular enhancement of the interface (especially now that there are options to reroot the the trees, I feel like adding bootstrap values is the last missing piece). If this will be done, I will definitely use it for my current project.

retrieving bootstrap values from a newick tree

This link provides two examples to how bootstraps are specified in newick trees (but maybe there are more ways?)

For example, iqtree (which we recently use a lot in the lab) abides to the first format mentioned in the link above (i.e. bootstrap_value:branch_length).

@meren, your opinion?

[meren]

If I am not mistaken, @ozcan has already made all the necessary changes for the interactive interface to be able to work with trees that contain bootstrap values. the problem is to display them in a meaningful way :/

[ozcan]

Hi @ShaiberAlon, Our parser already can parse trees with bootstrap values, we implemented that while ago but unfortunately we do not display bootstrap values anywhere besides mouse tab at the moment. I would like to sit and discuss this after the vacation if you have some ideas to display them. Best,

[ShaiberAlon]

That's great @ozcan !

I would love to discuss this, and I will think about it more. For now, I'll use this thread to collect my thoughts.

I saw this, and we could consider something like this for what seems to me like a simple approach: https://web.njit.edu/~usman/courses/bnfo602_spring18/root.jpg

In my opinion we should consider two things separately:

• How would people use this feature while using the interactive interface
• How would people use this when editing an SVG that they exported from the interactive interface.

[xvazquezc]

A very common way is using shapes/colours on the nodes. They are a common approach that many tree viewers incorporate, e.g. this https://media.nature.com/lw926/nature-assets/ismej/journal/v10/n10/images/ismej201643f2.jpg or this https://journals.plos.org/plosbiology/article/figure?id=10.1371/journal.pbio.1000602.g003

I'd also suggest to take a look to the controls in iTOL for ideas. It probably has way more controls than needed for anvi'o, but it can be a good source of inspiration.