Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with…

• NN
  National Natural Science Foundation of China

  Awards: HHSN272201400006C, U1601225
• SM
  Southern Medical University

  Award: G618289088
• NI
  National Institutes of Health

  Award: HHSN272201400006C
• SP
  Shenzhen Peacock Plan

  Award: KQTD201203