Is it possible to use gotree to add constrain information to a tree to prepare mcmctree input file about gotree HOT 3 CLOSED

xiekunwhy commented on July 30, 2024

Is it possible to use gotree to add constrain information to a tree to prepare mcmctree input file

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Comments (3)

xiekunwhy commented on July 30, 2024 1

Yes, that's what I want, and I think the following annotation file may produce the same results

B(79.2, 152.8, 1e-300, 1e-300):cma,dvi
B(89.7, 220.9, 1e-300, 1e-300):agl,dvi
B(152.3, 236.2, 1e-300, 1e-300):tmo,tca
B(250.999938, 302.8938, 0.025, 0.025):cma,ota

run

cat test.nwk|/Bio/User/kxie/software/mambaforge/envs/gotree/bin/gotree annotate -m annotation.txt --comment|tr '[' "'" | tr ']' "'"

I got

((((agl,(cma,dvi)'B(79.2, 152.8, 1e-300, 1e-300)')'B(89.7, 220.9, 1e-300, 1e-300)',sor),((tmo,zmo),tca)'B(152.3, 236.2, 1e-300, 1e-300)'),ota)'B(250.999938, 302.8938, 0.025, 0.025)';

The same.

Thank you very much~

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xiekunwhy commented on July 30, 2024

nwkit (https://github.com/kfuku52/nwkit) mcmctree command can do this but have bug (kfuku52/nwkit#7).

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fredericlemoine commented on July 30, 2024

Hi,

If you know the constraints for each node of the tree, one possibility may be to write an annotation file (annotations.txt):

B(79.2, 152.8, 1e-300, 1e-300):cma,dvi
B(89.7, 220.9, 1e-300, 1e-300):agl,cma,dvi
B(152.3, 236.2, 1e-300, 1e-300):tmo,zmo,tca
B(250.999938, 302.8938, 0.025, 0.025):tmo,zmo,tca,agl,cma,dvi,sor,ota

And attach the annotations as "comments" in the input tree:

echo "((((agl,(cma,dvi)),sor),((tmo,zmo),tca)),ota);" | gotree annotate -m annotations.txt --comment

It should give you a tree like this:

((((agl,(cma,dvi)[B(79.2, 152.8, 1e-300, 1e-300)])[B(89.7, 220.9, 1e-300, 1e-300)],sor),((tmo,zmo),tca)[B(152.3, 236.2, 1e-300, 1e-300)]),ota)[B(250.999938, 302.8938, 0.025, 0.025)];

In which you can just replace all '[' and ']' by ', for example:

echo "((((agl,(cma,dvi)),sor),((tmo,zmo),tca)),ota);" | gotree annotate -m annotations.txt --comment | tr '[' "'" | tr ']' "'"

Result:

((((agl,(cma,dvi)'B(79.2, 152.8, 1e-300, 1e-300)')'B(89.7, 220.9, 1e-300, 1e-300)',sor),((tmo,zmo),tca)'B(152.3, 236.2, 1e-300, 1e-300)'),ota)'B(250.999938, 302.8938, 0.025, 0.025)';

Does it answer your question?

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