# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "Rclade" in publications use:'
type: software
license: MIT
title: 'Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization'
version: 1.1.5
identifiers:
- type: doi
  value: 10.32614/CRAN.package.Rclade
abstract: Provides a single-function pipeline for automated collapsing and visualization
  of large phylogenetic trees with geological timescales. Automatically parses taxonomic
  labels from multiple formats (GTDB, Silva, NCBI, embedded, custom), identifies Most
  Recent Common Ancestors (MRCAs), assigns color-blind-safe palettes, executes batch
  collapsing with automatic nesting-aware ordering, integrates 'deeptime' geologic
  time scales with adaptive time breaks and unit switching, and manages smart legend
  layout. Supports special ancestral node identifiers (LUCA, LACA, LBCA) for highlighting
  key nodes in the tree of life. Provides external taxonomy file support for trees
  with incomplete or missing taxonomic labels. Features real-time logging with timestamps,
  step tracking, and multiple log levels. Includes comprehensive input validation
  for tree and sequence file formats. Reduces a 60-line manual workflow to a single
  function call while preserving full compatibility with the 'ggtree'/'deeptime' ecosystem.
  The visualization pipeline builds on 'ggtree' Yu et al. (2017) <https://doi.org/10.1111/2041-210X.12628>,
  'deeptime' Gearty (2025) <https://doi.org/10.1080/20964471.2025.2537516>, and 'ape'
  Paradis and Schliep (2019) <https://doi.org/10.1093/bioinformatics/bty633>.
authors:
- family-names: Zichao
  given-names: Zeng
  email: zengzichao@sjtu.edu.cn
preferred-citation:
  type: manual
  title: 'Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization'
  authors:
  - family-names: Zeng
    given-names: Zichao
    email: zengzichao@sjtu.edu.cn
  year: '2026'
  notes: R package version 1.1.2
repository: https://zengzichao.r-universe.dev
repository-code: https://github.com/zengzichao/Rclade
commit: 9a1a6288be471bd6abfea3e9ad9a3774030985bc
url: https://zengzichao.github.io/Rclade/
date-released: '2026-10-01'
contact:
- family-names: Zichao
  given-names: Zeng
  email: zengzichao@sjtu.edu.cn
references:
- type: article
  title: 'ggtree: an R package for visualization and annotation of phylogenetic trees
    with their covariates and other associated data'
  authors:
  - family-names: Yu
    given-names: Guangchuang
  - family-names: Smith
    given-names: David
  - family-names: Zhu
    given-names: Huachen
  - family-names: Guan
    given-names: Yi
  - family-names: Lam
    given-names: Tommy Tsan-Yuk
  year: '2017'
  journal: Methods in Ecology and Evolution
  volume: '8'
  issue: '1'
  doi: 10.1111/2041-210X.12628
  start: 28-36
- type: article
  title: 'deeptime: an R package that facilitates highly customizable and reproducible
    visualizations of data over geological time intervals'
  authors:
  - family-names: Gearty
    given-names: William
  journal: Big Earth Data
  year: '2025'
  doi: 10.1080/20964471.2025.2537516