Dating multiple trees --date-options "-n"

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Lars Berling

Apr 27, 2023, 5:40:52 PMApr 27

I am currently trying to simulate rooted time trees using IQ-tree.
The first thing I noticed when running with the "-b" option and the "--date... -o ..." options , is that the options to generate a rooted time tree are simply ignored and no time tree is generated at all.

Therefore, I am now generating my unrooted bootstrap trees first and then use the dating on the existing trees with the "-te" option.
This works fine for a single tree, i.e. I can run it with the "x.treefile" or on the "x.boottrees" files and get one rooted time tree.

However, I want every tree from the bootstrap sample to be a rooted time tree.
I found that I can use "--date-options '-n k' " to specify the number of trees.
-n datasetNumber
   The number of trees that you want to read and analyse.

But this does not work for k not equal to 1.
"iqtree -s alignment.phy -te alignment.phy.boottrees --date-tip 0 --date-root -1 -o 'OUT' -m GTR --date-options '-n 2' " --> ERROR: Error in input tree

"iqtree -s alignment.phy -te alignment.phy.boottrees --date-tip 0 --date-root -1 -o 'OUT' -m GTR --date-options '-n 1' " --> Works as expected

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