TreeShrink
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uym2
Implementation of the TreeShrink problem
Hello, any suggestion to solve this issue? Thanks for the help :) oscars@oscarpc:~/TreeShrink$run_treeshrink.py -t test_data/mm10.trees Launching TREESHRINK version 1.3.9 TREESHRINK was called as follow /home/oscars/anaconda2/bin/run_treeshrink.py -t test_data/mm10.trees Testing R and...
Hello I am very happy have this software can be used in my phylogenetic analysis, but there have some problems I can't fully understand。 1. What are the criterias for...
Hello, I am using Treeshrink to delete long branch in a SSU phylogeny. It does exactly what i want except that TreeShrink don't remove the species. I run: run_treeshrink.py -t...
Hi, I have been having an issue with TreeShrink deleting the node support values in the original tree files. I am using v1.3.5 on our HPC with R v3.4.5 and...
Hi Uyen, Many thanks again for implementing the "whitelisting" option! I would like to ask whether it would also be possible to implement an option to partition TreeShrink analyses by...
Dear Treeshrink, I have a loci.treefile with about 3800 gene trees. An issue arises due to gene trees with "too many taxa" when really, the genes are split in their...
Hi, I am getting an error message and wondered if it was related to the versions of python and R. I saw an earlier post also had issues using R...
Hello, Can we use R v4.0? I've just tried running the test data with R 4.0.1 and I get the error below. What version would you recommend? I'm using Python...
Hi, I have been having an issue with TreeShrink deleting the node support values in the original tree files. I am using v1.3.5 on our HPC with R v3.4.5 and...
Hi. I notice that when working with trees that have node label (e.g. from bootstrap support) the label from the random node where TreeShrink reroots the tree to do the...
