removes taxa on short branches

[bmichanderson]

Hi,
Thanks for creating this program!
I'm trying to use TreeShrink on 388 trees built for loci in my dataset, in order to detect and potentially remove taxa on long branches that may indicate assembly errors.

I built the program in a Singularity container which has Ubuntu 20.04 with python 3.8.10, R 3.6.3 and BMS 0.3.4 like so:

git clone https://github.com/uym2/TreeShrink.git
cd TreeShrink
python3 setup.py install
cd .. && rm -r TreeShrink

I ran TreeShrink on my trees file (from IQ-TREE) like so:

singularity exec -H "$(pwd)" phylo.sif run_treeshrink.py -t loci.treefile -m per-species -q 0.05 -O output_ts -o treeshrink

(note that the program issues warnings about BMS being built under R 4.0.3, though the BMS in the container was not; maybe I've messed something up here?)

I noticed strange behaviour for the first locus when I checked -- it dropped some long branches, but also some short branches, and it left some long branches intact.

The lines in the output files are:

Gene Species Taxon Signature
0 376716 376716 0.16188346887963004
0 376724Llin 376724Llin 0.16188346887963004
0 376683 376683 0.16188346887963004
0 376657 376657 0.16188346887963004
0 376745 376745 0.16188346887963004
0 376735 376735 0.07840338555281828
0 376770 376770 0.09844712647947677
0 376757 376757 0.05006538515754765
0 376774 376774 0.057018397312663276
0 376749 376749 0.04242609694816515
0 376778 376778 0.09844712647947677
0 376680 376680 0.09844712647947677
0 376729 376729 0.09844712647947677
0 376780 376780 0.09844712647947677
0 376750 376750 0.09844712647947677
0 376761 376761 0.09844712647947677
0 376677 376677 0.04242609694816515
0 376776Tcog 376776Tcog 0.04242609694816515
0 376718Llin 376718Llin 0.04242609694816515
0 376772 376772 0.04242609694816515
0 79740Tcog 79740Tcog 0.04242609694816515
0 376747 376747 0.04242609694816515
0 376725Llin 376725Llin 0.04242609694816515
0 376722Lmic 376722Lmic 0.027536231822437963

And for the actual deletions:

376724Llin      376745  376735  376778  376780  376761

I've created an image of the tree before (left) and after (right) TreeShrink, showing the dropped taxa in cyan and the "missed" taxa in red. Note the short branches dropped. I don't understand the summary file which doesn't seem to show any difference between a dropped taxon (e.g. 36724Llin) and one which was not dropped (e.g. 376716).

Any idea what is causing this behaviour?

[uym2]

Hello Ben, How many trees are there in the input file "loci.treefile"? If you don't have many trees, I suggest trying treeshrink in the "per-gene" mode. I can take a closer look if you can share with me the input trees and the output file of treeshrink. Thank you. Uyen

…

On Wed, Apr 26, 2023 at 3:35 AM Ben Anderson ***@***.***> wrote: Hi, Thanks for creating this program! I'm trying to use TreeShrink on 388 trees built for loci in my dataset, in order to detect and potentially remove taxa on long branches that may indicate assembly errors. I built the program in a Singularity container which has Ubuntu 20.04 with python 3.8.10, R 3.6.3 and BMS 0.3.4 like so: git clone https://github.com/uym2/TreeShrink.gitcd TreeShrinkpython3 setup.py installcd .. && rm -r TreeShrink I ran TreeShrink on my trees file (from IQ-TREE) like so: singularity exec -H "$(pwd)" phylo.sif run_treeshrink.py -t loci.treefile -m per-species -q 0.05 -O output_ts -o treeshrink (note that the program issues warnings about BMS being built under R 4.0.3, though the BMS in the container was not; maybe I've messed something up here?) I noticed strange behaviour for the first locus when I checked -- it dropped some long branches, but also some short branches, and it left some long branches intact. The lines in the output files are: Gene Species Taxon Signature0 376716 376716 0.161883468879630040 376724Llin 376724Llin 0.161883468879630040 376683 376683 0.161883468879630040 376657 376657 0.161883468879630040 376745 376745 0.161883468879630040 376735 376735 0.078403385552818280 376770 376770 0.098447126479476770 376757 376757 0.050065385157547650 376774 376774 0.0570183973126632760 376749 376749 0.042426096948165150 376778 376778 0.098447126479476770 376680 376680 0.098447126479476770 376729 376729 0.098447126479476770 376780 376780 0.098447126479476770 376750 376750 0.098447126479476770 376761 376761 0.098447126479476770 376677 376677 0.042426096948165150 376776Tcog 376776Tcog 0.042426096948165150 376718Llin 376718Llin 0.042426096948165150 376772 376772 0.042426096948165150 79740Tcog 79740Tcog 0.042426096948165150 376747 376747 0.042426096948165150 376725Llin 376725Llin 0.042426096948165150 376722Lmic 376722Lmic 0.027536231822437963 And for the actual deletions: 376724Llin 376745 376735 376778 376780 376761 I've created an image of the tree before (left) and after (right) TreeShrink, showing the dropped taxa in cyan and the "missed" taxa in red. Note the short branches dropped. I don't understand the summary file which doesn't seem to show any difference between a dropped taxon (e.g. 36724Llin) and one which was not dropped (e.g. 376716). Any idea what is causing this behaviour? [image: locus1] <https://user-images.githubusercontent.com/45042580/234502747-1ddc5132-3fb7-4af6-a618-f6ce973c2b77.png> — Reply to this email directly, view it on GitHub <#39>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB6MKWR7KDAD65HN7OBIXXDXDDF3TANCNFSM6AAAAAAXMA3VQA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[bmichanderson]

Hi Uyen,
I have 388 trees in the file. I'll try attaching the files here.
files.zip

[bmichanderson]

Hi again Uyen,
I've followed your advice and tried running in the "per-gene" mode. The results appear to be more consistent and to remove the long branches.
Cheers,
Ben