The tutorial script add_host_tips.R not working on FASTTREE or IQTREE version of the trees

[Jigyasa3]

Dear @BPerezLamarque ,

Thank you again for the add_host_tips.R script to add new host tips with branch lengths close to 0. I have been able to run this script successfully on a host tree from BEAST2. But when I run it using the version of the host tree from FASTTREE or IQTREE, I keep getting the following error and the edge length of the output tree is all NULL.

Error in if (where <= Ntip(tree) && position == 0) { : missing value where TRUE/FALSE needed

My files and version of the script used is here

[BPerezLamarque]

Hi @Jigyasa3,

It seems that the trees you generated using FASTTREE and IQTREE are not time-calibrated and contain branch lengths of 0 : you need to first calibrate these trees (e.g. using the chronos function in the R-package ape, or PATHd8 or treePL) to obtain calibrated trees. The function add_host_tips.R should work once you have calibrated trees. In addition, to run add_host_tips.R you need your trees to be in the "phylo" class, using "read.iqtree()" this is not the case, thus you must use "as.phylo()" to have the correct class.

All best, Benoît

[Jigyasa3]

Hi Benoit,

Thank you for your reply. I changed the edge.length value from Null to zero in the script. It generated a tree with the original edge lengths and zero edge lengths for added branches. Would I still need to calibrate the trees?

Thanks for the advice on as.phylo() object. I also added that to the script.

Regards, Jigyasa

On Wed, Jan 11, 2023, 8:11 PM Benoît Perez-Lamarque < @.***> wrote:

Hi @Jigyasa3 https://github.com/Jigyasa3,

It seems that the trees you generated using FASTTREE and IQTREE are not time-calibrated and contain branch lengths of 0 : you need to first calibrate these trees (e.g. using the chronos function in the R-package ape, or PATHd8 or treePL) to obtain calibrated trees. The function add_host_tips.R should work once you have calibrated trees. In addition, to run add_host_tips.R you need your trees to be in the "phylo" class, using "read.iqtree()" this is not the case, thus you must use "as.phylo()" to have the correct class.

All best, Benoît

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[BPerezLamarque]

Hi Jigyasa,

OK perfect. Yes you have to calibrate the tree before running add_host_tips.R because add_host_tips.R and then HOME require a time-calibrated tree.

All best, Benoît