Quantify support for branch nodes in tree reconstruction

[Will Hamilton]

Sorry if this is super obvious but I'd be very grateful for some help understanding how to extract information from the IQ-TREE output on the support for specific branch nodes (e.g. bootstrap values).

I am producing a tree from a multi-fasta alignment using ModelFinder + tree reconstruction (IQ-TREE 1.6.12 built Aug 15 2019). The terminal command looks like:

~/PATH/iqtree -s alignment_file -m MFP

I'm initially visualising the tree in FigTree but my question is about the IQ-TREE output. When I look at the .iqtree file there is an outline of the basic tree shape and a warning message: "near-zero internal branches (<0.0000) should be treated with caution/ Such branches are denoted by '**' in the figure below".

So it's a bit laborious but I can search for a sample manually in a text editor in this file to find its branch node, and then see whether there is ** at the branch or not. This gives me a qualitative sense of whether or not the branch is well supported. But what about a more quantitative output for a given branch e.g. its bootstrap value? 

Also, is there a more efficient way of searching for this information other than what I'm currently doing: looking at the tree (e.g. on FigTree or Microreact), deciding the branch I want to look at, control-F to find the sample ID next to the branch point in the .iqtree file, and checking whether there are ** next to that branch? Is it listed somewhere in a more searchable format?

Many thanks for your help.

Best wishes,

Will

[Minh Bui]

Hi Will,

On 10 Jul 2020, at 3:20 am, 'Will Hamilton' via IQ-TREE <iqt...@googlegroups.com> wrote:

Sorry if this is super obvious but I'd be very grateful for some help understanding how to extract information from the IQ-TREE output on the support for specific branch nodes (e.g. bootstrap values).

I am producing a tree from a multi-fasta alignment using ModelFinder + tree reconstruction (IQ-TREE 1.6.12 built Aug 15 2019). The terminal command looks like:

~/PATH/iqtree -s alignment_file -m MFP

Just note: you can actually omit -m MFP, as this is the default behaviour.

I'm initially visualising the tree in FigTree but my question is about the IQ-TREE output. When I look at the .iqtree file there is an outline of the basic tree shape and a warning message: "near-zero internal branches (<0.0000) should be treated with caution/ Such branches are denoted by '**' in the figure below".

So it's a bit laborious but I can search for a sample manually in a text editor in this file to find its branch node, and then see whether there is ** at the branch or not. This gives me a qualitative sense of whether or not the branch is well supported. But what about a more quantitative output for a given branch e.g. its bootstrap value? 

Normally such short branches will likely have low supports. So it’s OK if you just look at the bootstrap supports in FigTree.

You can use -czb option (in v1.6) or --polytomy option v2.0. This will collapse all near-zero branches in the final tree, so that it may become multifurcating. 

Also, is there a more efficient way of searching for this information other than what I'm currently doing: looking at the tree (e.g. on FigTree or Microreact), deciding the branch I want to look at, control-F to find the sample ID next to the branch point in the .iqtree file, and checking whether there are ** next to that branch? Is it listed somewhere in a more searchable format?

OK, I think the options mentioned above will help?

Minh

Many thanks for your help.

Best wishes,

Will

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[Will Hamilton]

Hi Minh,

Thanks for your reply.

So how can I see the bootstrap values in FigTree, if I import the IQ-TREE .treefile? If I click "node labels" I can see numbers by each branch - are these the bootstrap values? I'm expecting to see a value between 0 and 1 for proportion of trees tried that had the same branch node there.

Thanks for your help, and best wishes,

Will

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--

William L. Hamilton MRCP PhD

CMT Academic Clinical Fellow

Cambridge University Hospitals NHS Foundation Trust

[Minh Bui]

Hi Will,

The bootstrap values are in percentage, between 0 and 100%. In FigTree, In the "Node Labels” tab, click “Display" and choose “label”. Otherwise, FigTree displays in the “Node ages” by default, which is not what you want.

Cheers

Minh

To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/CAHBmnkkGmneEHfbA91apKzCmTnGgutGZ_D5xTDMp7ANikfKT3A%40mail.gmail.com.

[Will Hamilton]

Hi Minh,

Under the "Node labels" tab, in the "Display" box my options are: Node ages, Node heights (raw), Branch times, and Branch lengths (raw). I don't have a "label" option here? And none of the options I've listed seem to give sensible numbers as a percentage between 0-100%. Sorry if I'm missing something obvious!

Best Wishes,

Will

To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/69948E90-69D1-46C7-9E6F-E470FFEAB0DD%40univie.ac.at.

[Minh Bui]

Oh, This is because you didn’t perform bootstrap, that’s something I missed from your first email. Please continue to read the tutorial in the bootstrap section, http://www.iqtree.org/doc/Tutorial

Minh

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