wrong mrca age when nexus file contains translate block

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Michael Matschiner

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Sep 27, 2018, 6:04:24 AM9/27/18
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Hi all,

I noticed that for one particular node of a tree that I'm reading from a nexus file, the wrong age is reported by tree.mrca(taxon_labels=taxon_labels). This only occurs when the nexus file includes a translate block but not without. The two nexus files (tmp2.tre; without translate block, and tmp3.tre; with translate block) and the script that I used (get_mrcas.py) are attached. I'm using DendroPy v.4.4.0, and I start the script with this command:

$ python3 get_mrcas.py -t tmp2.tre -s arcgla_spc mermer_spc
7.246093

$ python3 get_mrcas.py -t tmp3.tre -s arcgla_spc mermer_spc
8.559984175048072

7.246093 is the age of the second-oldest node in the phylogeny (which is the mrca of the taxa arcgla_spc mermer_spc), 8.559984175048072 is the age of the root node.

Any idea why this could be?

Cheers,
Michael
tmp2.tre
tmp3.tre
get_mrcas.py

Jeet Sukumaran

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Sep 27, 2018, 3:01:58 PM9/27/18
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Tree "tmp2.tre" is treated as rooted, due to the "[&R]" token, while
tree "tmp3.tre" is treated us unrooted due to lack of this token.

Coercing both trees to be treated as rooted (``rooting="force-rooted"``)
or unrooted (``rooted="force-unrooted"``) gives the same results for
both trees.

Rooting state matters.

-- jeet
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Michael Matschiner

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Sep 27, 2018, 5:01:27 PM9/27/18
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Thanks a lot, Jeet, for the fast response. Very helpful!

Cheers,
Michael
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