treeio: Base classes and functions for parsing and exporting phylogenetic tree
Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.
treeio was splitted from
ggtree package, please cite the following
article when using
G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36.
treeio is easy, follow the guide on the Bioconductor
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") ## biocLite("BiocUpgrade") ## you may need this biocLite("treeio")
Supported tree format:
- New Hampshire eXtended format (NHX)
Supported software output:
merge_treefor merging evolutionary evidences inferred from different phylogenetic analyses
Find out details and examples on Documentation.
Projects that depend on treeio
- harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities
- LINC: co-expression of lincRNAs and protein-coding genes
- LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors
- philr: Phylogenetic partitioning based ILR transform for metagenomics data
- Please make sure you have followed the important guide before posting any issue/question
- For bugs or feature requests, please post to github issue
- For user questions, please post to google group
- We are also following every post tagged with treeio on Bioconductor support site and Biostars
- Join the group chat on and