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YuLab-SMU
:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
Hi, When converting from igraph to phylo, I run into the issue of C stack overflow for very deep trees. Reproducible example: [tree_final_1.rds.zip](https://github.com/YuLab-SMU/treeio/files/8551338/tree_final_1.rds.zip) ``` > tree = readRDS('tree_final_1.rds') > treeio::as.phylo(tree)...
Add filter methods for placement filtering: "all","max_lwr","max_pendant", "min_likelihood","lwr","pendant","likelihood"
### Describe you issue * [ ] I import a nkw file as read.newick(".nwk") * [ ] I construct this file with PopPUNK to habe GPSC * [ ] I...
Hello everyone, I used CodeML in PAML through the graphical user interface PamlX to estimate branch lengths for a phylogeny of orthologous proteins given a known species tree. Also, I...
I am having an issue when loading and trying to plot one of my MCC trees from a BEASTv1.10.4 run. Here is the link to my R code: https://gist.github.com/taylorpaisie/0c8b07d81003419d94426bfe814ea4ff Here...
Thank you for the excellent packages! I was wondering if it would be possible to implement functionality that would enable the importing of MCMCTree 'nexus' result trees, and their subsequent...
Dear author and users, ``` axmlng_phylo
Dear @GuangchuangYu I recently use ggtree to process my phylogenetic tree. I obtained the tree file through IQTree and exported the file in nexus format by figtree. But I meet...
Hello Dr. Yu, Thanks for this incredible package! The function read.beast allows me to read either single (class: treedata) or multiple BEAST trees (treedata list). However, the function write.beast only...
Hi, Thank you for a fantastic resource. I was wondering if there's a way to drop tips from a BEAST tree after reading in with read.beast? Thank you in adavance,
