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uym2 / TreeShrink

Implementation of the TreeShrink problem
https://uym2.github.io/TreeShrink/
GNU General Public License v3.0
36 stars 11 forks source link

Whitelisting of important taxa #24

Closed BenKuhnhaeuser closed 3 years ago

BenKuhnhaeuser commented 4 years ago

Hi Uyen, Would it be possible to implement an option for "whitelisting" important taxa that should not be removed? In particular, I am thinking about protecting outgroups from pruning when per-species mode is not possible due to low occupancy of some taxa, which caused in my case the removal of outgroup taxa from over 700 out of ca. 1000 gene trees, respectively (whereas in per-species mode, the outgroup taxa were removed from less than 50 gene trees, respectively). Best, Ben

uym2 commented 4 years ago

Hello Ben,

Thank you for a good suggestion. I have added the feature in the new release (v1.3.6): with -x you can just list out the "important" species , which will never be removed. To list multiple species, you can put them in a quote, for example, -x "sp1 sp2 sp3" or put them in a file, for example -x important_species.txt

I hope the software would be helpful for you.

Best, Uyen

BenKuhnhaeuser commented 4 years ago

Hi Uyen,

Fantastic, thank you very much! That's exactly what I was after.

Best, Ben

BenKuhnhaeuser commented 3 years ago

Hi Uyen,

I have now tested the new -x option, and it seems to work very well. I noted just one little thing: the output message from TreeShrink still says that the whitelisted taxon was removed although it wasn't - so that might cause a little confusion. An example:

Launching TREESHRINK version 1.3.6 TREESHRINK was called as follow /TreeShrink_1.3.6/run_treeshrink.py -i treeshrink_dir -t input.tree -a input.fasta -x Calamus-castaneus-RBL220 -m per-species ... Calamus-castaneus-RBL220: will be cut in 32 trees where its impact is above 1.726009 for quantile 0.05

Best, Ben

uym2 commented 3 years ago

Hello Ben,

Thanks for letting me know, I will fix the message of TreeShrink. I am glad you find the program helpful.

Best, Uyen

On Friday, November 27, 2020, Benedikt Kuhnhäuser notifications@github.com wrote:

Hi Uyen,

I have now tested the new -x option, and it seems to work very well. I noted just one little thing: the output message from TreeShrink still says that the whitelisted taxon was removed although it wasn't - so that might cause a little confusion. An example:

Launching TREESHRINK version 1.3.6 TREESHRINK was called as follow /TreeShrink_1.3.6/run_treeshrink.py -i treeshrink_dir -t input.tree -a input.fasta -x Calamus-castaneus-RBL220 -m per-species ... Calamus-castaneus-RBL220: will be cut in 32 trees where its impact is above 1.726009 for quantile 0.05

Best, Ben

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-- Uyen

uym2 commented 3 years ago

Fixed in v1.3.7