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YuLab-SMU
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treeio
:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
https://yulab-smu.top/treedata-book/
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read.nextstrain.json fails on divergence trees
#126
CecileTK
opened
3 weeks ago
0
tree_subset function no longer exists in the recent release of treeio
#125
NPSDC
opened
2 months ago
1
phyloXML and missing branch lengths
#124
jvolkening
opened
6 months ago
0
Update CITATION
#123
Clearmind777
closed
6 months ago
0
[feature request] `text=` argument for `read.raxml` function
#122
Fan-iX
opened
6 months ago
0
read.raxml() parsing error
#121
gunjanpandey
opened
7 months ago
0
root function loses tip.label and node.label
#120
jayoung
opened
8 months ago
5
Issue with drop.tip function in removing node C from tree structure A->B->C
#119
moqi111
opened
8 months ago
1
speed up read.beast
#118
SimonGreenhill
closed
7 months ago
2
make write.jtree more efficient and less noisy
#117
SimonGreenhill
closed
7 months ago
0
fix test warnings
#116
SimonGreenhill
closed
7 months ago
2
add write.jplace
#115
xiangpin
closed
8 months ago
0
read.iqtree and regular bootstrap
#114
LPDagallier
opened
9 months ago
0
added support for multiple trees / writing phylo objects in write.beast
#113
brj1
closed
3 months ago
2
No write.jplace function?
#112
adriaaula
closed
8 months ago
1
support for LSD2 dating file import
#111
sihellem
opened
10 months ago
2
reexport as.phylo.hclust_node
#110
xiangpin
closed
11 months ago
0
S3 overwrite warning in R version 4.3.1 (2023-06-16) with treeio 1.24.3
#109
ckeeling
opened
11 months ago
2
Just wonder, are the functions drop.tip() and tree_subset() same in mathematics?
#108
judyssister
opened
11 months ago
0
use check_installed to check whether the suggest pkgs is installed
#107
xiangpin
closed
1 year ago
1
fix issue when beast file contain negative branch
#106
xiangpin
closed
1 year ago
1
update spt and as.phylo.igraph consider edge attributes and add find.hclust.igraph
#105
xiangpin
closed
11 months ago
2
Functions.migrate
#104
xiangpin
closed
11 months ago
0
suppress the warning message about check whether is a tbl_tree
#103
xiangpin
closed
1 year ago
0
add find.spt funtion
#102
xiangpin
closed
1 year ago
0
fix a bug of as.treedata for tbl_df
#101
xiangpin
closed
1 year ago
0
Keep.tip
#100
xiangpin
closed
1 year ago
0
convert igraph to phylo
#99
xiangpin
closed
1 year ago
0
"elf_dynamic_array_reader.h:61 tag not found" when loading an iqtree file
#98
vmkalbskopf
opened
1 year ago
2
fix a bug in read.nhx when the string of metadata contains the character and numeric simultaneously
#97
xiangpin
closed
1 year ago
0
read.nhx() bug
#96
X1angyang
closed
1 year ago
3
supporting dendro class to phylo class
#95
xiangpin
closed
1 year ago
0
treeio_1.22.0 not found in https://bioconductor.org/packages/3.15
#94
nick-youngblut
closed
1 year ago
1
add Inner_join method
#93
xiangpin
closed
1 year ago
0
update full_join method
#92
xiangpin
closed
1 year ago
0
as.treedata sequence length
#91
antoine4ucsd
opened
1 year ago
1
Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
#90
teng-gao
closed
1 year ago
2
problem
#89
svedwards
closed
1 year ago
1
update as.phylo and as.treedata method for data.frame class
#88
xiangpin
closed
1 year ago
0
as.treedata creating label.x and label.y columns in some cases
#87
nick-youngblut
opened
1 year ago
0
add as.phylo for list
#86
xiangpin
closed
1 year ago
2
Add filter method to get.placement()
#85
mjchen1996
opened
1 year ago
7
To better support the visualization of pvclust class using ggtree
#84
xiangpin
closed
1 year ago
0
Add filter method to get.placement.jplace
#83
mjchen1996
closed
1 year ago
0
update as.treedata for pvclust
#82
xiangpin
closed
1 year ago
0
add read.nextstrain.json
#81
xiangpin
closed
2 years ago
0
Error in check_edgelist(x) : Cannot find root. network is not a tree!
#80
acpaulo
closed
1 year ago
2
rename tip label by a mapping table for multiphylo tree
#79
neptuneyt
closed
2 years ago
3
as.phylo C stack overflow caused by deep trees
#78
teng-gao
opened
2 years ago
11
Error in tests due to get_aes_var
#77
maelle
closed
2 years ago
3
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