Phylogenetic dating

[Mahin Chavoshi]

Hi there,

I am writing to ask a question related to phylogenetic dating-Calibrating tree using ancestral dates-Dating an existing tree. I only have one node (root) to calibrate and with IQtree options I tried to run the analysis:

 /apps/iqtree/2.0.7/bin/iqtree2 -s alignment.phy -spp partitions.txt --date datefile.txt -te Tree_File.tre,

 but it returns this error: constraints provided are not enough, or conflict. Minimum branch length is then set to 0.

am I missing something with this analysis?

Many thanks,

Mahin

[Hien To]

Hi Mahin,

Sorry I didn’t see your email before. I guest that your file datefile.txt defines only the calibration node and doesn’t contain the tip nodes? So you should specify the tip nodes to 0 with option   --date-tip 0. And remember that in our timed tree, a node always has date >= its ancestral’s date. So if the calibration point is, for example, 2 my ago, then it should be specified as -2 in the date file. 

Lots of people confuse about those input dates specifications, so I think I will change those to make them easiser for users.

Cheers,

Hien

On Tue, 10 Aug 2021 at 8:23 am, Minh Bui <minh...@univie.ac.at> wrote:

Hi Hien, can you answer this question too?

Minh

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