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:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
I get a warning every time I start RStudio before any code has been executed: ``` Registered S3 methods overwritten by 'treeio': method from MRCA.phylo tidytree MRCA.treedata tidytree Nnode.treedata tidytree...
Hi, IQ-TREE added least square dating (LSD2) method to build a time tree (http://www.iqtree.org/doc/Dating). The produced dated tree (.timetree.nex file) looks a lot a BEAST timetree. Using treeio::read.beast() does not...
For example, tree0 could be divided into subtree1 and subtree2. If extracting subtree1 using tree_subset() equals to that deleting all tips of subtree2 from tree0?
That is the error when I try to load an iqtree file in RStudio. If I try to load it in a base R session, I get this: ` ***...
hello thank you for your nice package I am trying to use it in order to plot my tree along with aminoacid sub (with ggtree). My input are a nt...
I recently updated R and accordingly treeio, and I no longer see `tree_subset` function being exported by the package. Is there a reason why it is not there? I could...
Hello, I have made a pml tree similar to section 1.3.3 in your vignette. However, when I get to > pmltree Error in UseMethod("as.treedata") : no applicable method for 'as.treedata'...
### Description of the issue I've recently faced issues when using the function ```read.nextstrain.json``` on divergence trees (with divergence units in number of mutations). When using it on a json...
