Constrain trees with branch lengths

[Sergio Andrés Muñoz Gomez]

Dear Minh,

I've been using constrained trees for some tree searches, but I was not mindful about the branch lengths I left for the constraints. I recently run a edge-unlinked partitioned analysis and it appears that the branch lengths for all partitions are the same. I now wonder if using a constraint with branch lengths forces IQTREE to also constrain branch lengths on top of the topology itself.

I would appreciate it lots if you can clarify this to me.

Thanks,

[Bui Quang Minh]

Hi Sergio,

On Nov 2, 2017, at 3:27 PM, Sergio Andrés Muñoz Gomez <sergi...@gmail.com> wrote:

Dear Minh,

I've been using constrained trees for some tree searches, but I was not mindful about the branch lengths I left for the constraints. I recently run a edge-unlinked partitioned analysis and it appears that the branch lengths for all partitions are the same. I now wonder if using a constraint with branch lengths forces IQTREE to also constrain branch lengths on top of the topology itself.

No, the constraint only forces the tree topology to obey it. Branch lengths are free to vary. So if what you described is true, then it’s weird. To be sure, please send me the command line and the log file. I will have further look.

Thanks, Minh

I would appreciate it lots if you can clarify this to me.

Thanks,

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Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

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