IQ-TREE configuration: consensus tree creation with 5 newick tree files

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Hi, I’m trying to create a consensus tree from five Newick tree files that I generated with IQ-TREE, but I don’t really understand how to do that. Could someone help me with this ? :slight_smile:

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Hi @Fernando_Martin

Please find the options for generating a consensus on the tool form here. It is a bit nested but hopefully the screenshot helps! The idea is to input the current trees, then to use this option when running through the same tool again.

iq-tree-consensus-options
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The :graduation_cap: Galaxy Training Network (GTN) has some tutorials that go over the data commonly used for evolution and tree building algorithms.

Be sure to check the :globe_with_meridians: Available on these Galaxies pull-down at the top of tutorials to learn which public servers are currently hosting the tools. Or, you can check under the Evolution section of the tool panel. Galaxy also hosts tools under Visualization for exploring and graphing.

The tool forms also have condensed Help. Most of what you can do with the original tool can also be done in Galaxy!

Reviewing 5.8 Consensus construction and bootstrap value assignment in http://www.iqtree.org/doc/iqtree-doc.pdf

The corresponding section in the tutorial can be found at

Please give this a review! Follow-up questions are welcome. :slight_smile:

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Hi @jennaj ,

thanks for the quick reply! I ran it with the consensus tree parameters but it gives the following error:

            ERROR: Unknown sequence format, please use PHYLIP, FASTA, CLUSTAL, MSF, or NEXUS format

How I understood it from the documentation “http://www.iqtree.org/doc/iqtree-doc.pdf” you should be able to pass the Newick tree files, which is something I did

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Here is the link to the Galaxy history: Galaxy

Thanks in advance :slight_smile:

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Thanks for sharing the history @Fernando_Martin very helpful!

It seems the full consensus option hasn’t been wrapped into the Galaxy tool yet. The current implementation requires sequences.

For now, you can either run everything together into one batch, or do that plus include the prior results to map the values across runs (Specify an input “target” tree file).

From here, we can try to get input from one of the developers. Ping @bernt-matthias what do you think? Is there an alternative available? Should we open a new request ticket to the IUC?

Thanks and let’s see what they think! :slight_smile:

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Hi I created IQtree implement consensus tree generation from trees · Issue #7912 · galaxyproject/tools-iuc · GitHub

Can you share the history/dataset where you got theUnknown sequence format error?

Currently the tool allows only nhx dataset as input for -t. Could you supply multiple trees with a single nhx file? I think this should work

Your goal would be to allow different formats, e.g. one newick file containing multiple trees?

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Now I have seen the history :sweat_smile:

Looks like your nhx datasets are actually newick. How have thy been generated? A Galaxy tool or upload?

You could try to concatenate them an change the datatype to newick?

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Hi Bernt,
They have been generated with core genome alignments from pangenome analysis tools that were then used in IQ-TREE. So the files you see are actually IQ-TREE output tree files.

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I was wrong again: `nhx` is actually (an extended form of) newick. So this is fine.

When looking at your history I noticed that you input the trees to the parameter Specify input alignment file but you actually should input them to Specify a file containing starting tree for tree search.

So I guess you could try to concatenate your trees into one data set and input them into the tool via `Specify a file containing starting tree for tree search` (note the `-t` below the parameter which indicates the actual command line parameter … which is also referred to by the consensus parameters). Let us know if this works.

IMO Galaxy should not have allowed to input the nhx format into the alignment parameter. The problem is that it accepts generic `txt`. I will suggest to change this.

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Hi Bernt,
I input the files as one concatenated dataset via Specify a file containing starting tree for tree search and got the following error:

            Invalid "--contree" option.
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This is a bug in the wrapper. A fix will be included in iqtree updates by bernt-matthias · Pull Request #4724 · galaxyproject/tools-iuc · GitHub .. should arrive soon on the usegalaxy instances. Should then be version 2.4.0+galaxy2

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Great, thank you very much!
Cheers