uym2
commented
3 years ago 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 is 0.05; you may want to try rerunning with -q 0.1 (or higher).
Thanks, Uyen
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 Constained-tree.tre
The long branch are well identified:
tree_treeshrink/output_summary.txt Gene Species Taxon Signature 0 Anabaena_sp._GCA_001672195.1 Anabaena_sp._GCA_001672195.1 0.7360354460973264 0 Anabaena_sp._GCF_009498015.1 Anabaena_sp._GCF_009498015.1 0.7360354460973264 0 Hapalosiphonaceae_cyanobacterium_GCA_003261315.1 Hapalosiphonaceae_cyanobacterium_GCA_003261315.1 0.7360354460973264 0 Fischerella_thermalis_GCF_002870635.1 Fischerella_thermalis_GCF_002870635.1 0.7360354460973264 0 Nostoc_sp._GCA_003326205.1 Nostoc_sp._GCA_003326205.1 0.7360354460973264 0 Nostoc_minutum_GCA_003326215.1 Nostoc_minutum_GCA_003326215.1 0.7360354460973264 0 Nostoc_sp._GCF_002155185.1 Nostoc_sp._GCF_002155185.1 0.7360354460973264 0 Fischerella_sp._GCF_000517105.1 Fischerella_sp._GCF_000517105.1 0.7360354460973264 0 Trichormus_sp._GCF_001858025.1 Trichormus_sp._GCF_001858025.1 0.23990056815295854 0 Calothrix_desertica_GCF_007830875.1 Calothrix_desertica_GCF_007830875.1 0.045563374212597145 0 Gloeobacter_violaceus_GCF_000011385.1 Gloeobacter_violaceus_GCF_000011385.1 0.2171282618054408 0 Gloeobacter_kilaueensis_GCF_000484535.1 Gloeobacter_kilaueensis_GCF_000484535.1 0.2171282618054408
But the output tree still contains these species (output.txt is empty), How can i do to force the delete ?
Luc