Uyen Mai comments

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                                            Uyen Mai

No support values in output trees

Hello PeteCowman, We have purposely removed the support value after the filtering, that is because the support values will change when remove some species. We also highly recommend that you...

Python and R version compatibility

Hello everyone, We are working to use Python's Scipy instead of R to do statistical tests, so we will bypass this issue. Currently, there is a pre-release (v1.3.8b) available [here](https://github.com/uym2/TreeShrink/releases/tag/v1.3.8b)....

run_treeshrink.py fails with python 3.10

Thank you very much for pointing out the error snf fixing it. I will do some tests and will merge. On Thu, Apr 27, 2023 at 5:42 AM V-Z ***@***.***>...

Node label transfer error at rooting point

Hello Diego, Thank you for pointing out the issue. Because the bootstrap support would not make sense after the tree has some taxa removed, we do not keep track of...

Error in rank(x, ties.method = "min", na.last = "keep") : unimplemented type 'list' in 'greater'

Can you send me the tree? It helps a lot in debugging. You can send to my email [email protected]. Thank you!

Can R v4 be used?

Hi Paul, Thanks for letting us know about the issue. I will soon update TreeShrink to work with R v4. Best, Uyen

Single gene - delete long branch

Hello Luc, The output_summary.txt file lists all the *potential* long branches, but the actual deletion is determined by -q. Did you specify -q in your run? If not, the default...

removes taxa on short branches

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...