YuLab-SMU / treeio

:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output

https://yulab-smu.top/treedata-book/

YuLab-SMU/treeio Issues

tree_subset function no longer exists in the recent release of treeio
Updated 25 days ago
Issue with function write.beast: not writing multiple BEAST trees
Closed 2 months ago4
phyloXML and missing branch lengths
Updated 4 months ago
S3 overwrite warning in R version 4.0.3
Closed 3 years ago7
[feature request] `text=` argument for `read.raxml` function
Updated 5 months ago
read.raxml() parsing error
Updated 6 months ago
root function loses tip.label and node.label
Updated 6 months ago5
Issue with drop.tip function in removing node C from tree structure A->B->C
Updated 6 months ago1
No write.jplace function?
Closed 6 months ago1
read.iqtree and regular bootstrap
Updated 8 months ago
S3 overwrite warning in R version 4.3.1 (2023-06-16) with treeio 1.24.3
Updated 8 months ago2
support for LSD2 dating file import
Updated 8 months ago2
Just wonder, are the functions drop.tip() and tree_subset() same in mathematics?
Updated 10 months ago
"elf_dynamic_array_reader.h:61 tag not found" when loading an iqtree file
Updated a year ago2
as.treedata sequence length
Updated a year ago1
Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Closed a year ago2
problem
Closed a year ago1
Error in check_edgelist(x) : Cannot find root. network is not a tree!
Closed a year ago2
read.nhx() bug
Closed a year ago3
Error while reading mlc file from CODEML
Updated a year ago2
treeio_1.22.0 not found in https://bioconductor.org/packages/3.15
Closed a year ago1
as.treedata creating label.x and label.y columns in some cases
Updated 2 years ago
as.phylo C stack overflow caused by deep trees
Updated 2 years ago11
It takes too much time for reading large tree file.
Closed 2 years ago1
rename tip label by a mapping table for multiphylo tree
Closed 2 years ago3
Error in tests due to get_aes_var
Closed 2 years ago3
Issue with the read.paml_rst function while reading rst file from CodeML/PAML
Updated 3 years ago
Issue with loading MCC tree from BEAST v 1.10.4
Updated 3 years ago4
read.bease fails to load NEXUS tree files with spaces in tip labels
Closed 3 years ago2
Error when convert tibble into tree with as.treedata or as.phylo: check_edgelist
Closed 3 years ago
drop.tip with method=="treedata" ignores additional parameters
Closed 3 years ago
Feature Request: Import MCMCTree Result Tree (PAML)
Updated 3 years ago4
read.beast() adding brackets and part of taxa to @data classifiers in v1.15.7
Closed 3 years ago
tbl_tree object to phylo object lost bootstrap column
Updated 3 years ago2
treeio read tree files form nexus format with extra quotation marks
Updated 3 years ago3
Regarding "read.beast" function
Closed 3 years ago2
Drop tips for BEAST trees
Updated 4 years ago1
error while reproducing manual example
Closed 4 years ago8
as.treedata is not compatible with merge manipulation?
Closed 4 years ago4
Reading RAxML-ng trees - coerce phyla to data.frame
Closed 4 years ago3
tree::offspring returns empty table with self_include = T
Closed 4 years ago2
could not find function "read.mega"
Closed 4 years ago3
Mapping between phylogenetic tree edge table and the placement post-traversal edge
Updated 4 years ago
Node Field in read.jplace()
Updated 5 years ago2
Error: `by` can't contain join column `label` which is missing from RHS when rename tip lable
Closed 5 years ago1
No MRCA function in treeio_1.8.1
Closed 5 years ago1
Reading raxml-ng trees with bootstrap support
Closed 5 years ago4
Error loading RAxML file
Closed 5 years ago4
treeio:::root.phylo doesn't seem to work and is not compatible with ape::root.phylo
Closed 5 years ago1
groupOTU.treedata currently drops all related data
Closed 6 years ago1