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YuLab-SMU
:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
Hello everyone!! I'm trying to read an mlc file (output from CODEML program) using the `read.codeml_mlc` function. However, I'm getting the following error: ``` tree
I have done the following experiment: I have a reference tree which was generated from full length 16S rRNA sequences. I took these long sequences that were used to build...
Hello, First thanks for publishing Treeio - very helpful set of code. I do have a question about a field that is present from get placements(). I have a .jplace...
The expected result of using `as.treedata`, according to the example in the function docs: ``` library(ape) library(dplyr) set.seed(2017) tree
### Prerequisites + [x] Have you read [Feedback](https://guangchuangyu.github.io/software/treeio/#feedback) and follow the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)? * [x] make sure your are using the latest release version * [x] read the [documents](https://guangchuangyu.github.io/software/treeio/documentation/) * [x]...
### Prerequisites - [x] make sure your are using the latest release version - [x] read the [documents](https://guangchuangyu.github.io/software/treeio/documentation/) - [x] google your quesion/issue ### Describe you issue Sometimes I have...
I aligned protein sequences with `raxml -T 32 -s sequences.aln -n pinA.output -m PROTGAMMABLOSUM62 -f d -b 1 -N 100 -p 1 -d` but while trying to load the ```RAxML_bootstrap.pinA.output```...
hi there, I am trying to reroot a treedata object, and I find that the tip.label and node.labels are getting lost from the phylogeny (they're getting replaced with `c("1","2","3",etc)` The...
## Problem Description I am working with a tree structure where nodes are labeled as A->B->C. I am attempting to use the `drop.tip` function to remove node C from the...
Hi, Let's take the case were a tree has been inferred with IQTREE, but branch support was assessed with non-paramteric bootstrap (BS) and not with UFBoot or SH-alrt. I just...
