"-sup command": more (informative) options?

[max maronna]

Hello,
I´m testing the IQTREE options, and I think that one nice option would be even more informative (in p19 the manual said):

"Finally, an useful feature is to read in an input tree and a set of trees, then IQ-TREE can assign the support value onto the input tree (number of times each branch in the input tree occurs in the set of trees) by:
iqtree -sup input_tree set_of_trees"

I think it would be useful (and informative) to identify from which tree (from the set_of_trees file) a certain branch is represented. This idea comes from the navajo rug strategy (something like the cladescan approach https://rc.fas.harvard.edu/resources/documentation/software/cladescan/ )...
maybe a combined result would be informative too! (% from total trees@and tree(s) order(s) in the mentioned set_of_trees file: 75@1@2@4 -considering a total of 4 trees-).

Best,
max

[Bui Quang Minh]

Dear Max, 

such an option should be relatively easy to implement. Just to be sure: I can append node labels with ‘@id’ series, where id is the index of tree where the corresponding clade occurs. Such information can then be viewed with tree viewing programs like Figtree.

When do you want to use such feature?

Cheers, 

Minh

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Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Max F. Perutz Laboratories

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 24026

Fax: ++43 1 4277 24098

Email: minh.bui (AT) univie.ac.at

[max maronna]

Hello Minh, thanks for the fast response!

Besides FigTree, I prefer the TreeGraph program http://treegraph.bioinfweb.info/
I would like to use  the aforementioned option with the -sup command, maybe adding an extra tag, being explicit that we want to identify the @tree(s) where a certain branch is represented....
example

normal way
iqtree -sup input_tree set_of_trees

with a tag for "extra info"
iqtree -sup @tag input_tree set_of_trees

I think this options would be useful to compare_summarize a main result ("input_tree"; eg, a multilocus analysis) with several types of "set_of_trees", like

1. single gene analysis;
2. traditional (previous) systematic proposals for the group;
3. alternative results, i) using different evolutionary models, ii) partitioned vs non-partitioned datasets, iii) masking vs non-masking datasets.

In most cases, differences between some alternative topologies are concentrated just in some branches: that´s the reason why I think it would be useful to "tag" these differences.

Others options I think would be interesting to see in IQTREE:

> Partitioned support (like raxml´s option "-f J" combined with "-M" for Sh-like support)

> alRT and aBAYES support method (from PhyML), including a partitioned version.

Best,

max

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[Bui Quang Minh]

Dear Max, I added this into the TODO list. Will get back to you in case something pops up.

Cheers, Minh

[max maronna]

Hello Minh,
great!

Thanks for your fast response (and interest in our opinions)!!!

best,

max