Rclade Third-Party Software and Data Notices
==============================================

This file lists all third-party software packages and data bundled with or
referenced by Rclade, along with their licenses and citation information.

Rclade itself is licensed under the MIT License (see LICENSE file).
Rclade uses third-party packages via API calls only; no third-party source
code has been copied into this project.

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R Package Dependencies (Imports)
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ape (>= 5.0)
  License: GPL-2 | GPL-3
  Citation: Paradis E, Schliep K (2019). "ape 5.0: an environment for
    modern phylogenetics and evolutionary analyses in R." Bioinformatics,
    35(3), 526-528. doi:10.1093/bioinformatics/bty633
  URL: https://ape-package.ird.fr/

ggtree (>= 4.0.0)
  License: Artistic-2.0
  Citation: Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y (2017). "ggtree: an R
    package for visualization and annotation of phylogenetic trees with
    their covariates and other associated data." Methods in Ecology and
    Evolution, 8(1), 28-36. doi:10.1111/2041-210X.12628
  URL: https://bioconductor.org/packages/ggtree/

deeptime (>= 1.0)
  License: GPL (>= 3)
  Citation: Gearty W (2025). "deeptime: an R package that facilitates
    highly customizable and reproducible visualizations of data over
    geological time intervals." Big Earth Data.
    doi:10.1080/20964471.2025.2537516
  URL: https://williamgearty.com/deeptime/

ggplot2 (>= 3.5.0)
  License: MIT + file LICENSE
  Citation: Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis.
    Springer-Verlag New York. ISBN 978-3-319-24277-4.
  URL: https://ggplot2.tidyverse.org/

rlang
  License: MIT + file LICENSE
  Citation: Henry L, Wickham H (2026). rlang: Functions for Base Types
    and Core R and 'Tidyverse' Features. R package.
  URL: https://rlang.r-lib.org/

stringr (>= 1.5)
  License: MIT + file LICENSE
  Citation: Wickham H (2025). stringr: Simple, Consistent Wrappers for
    Common String Operations. R package.
  URL: https://stringr.tidyverse.org/

tidytree (>= 0.4)
  License: Artistic-2.0
  Citation: Yu G (2022). Data Integration, Manipulation and Visualization
    of Phylogenetic Trees (1st edition). Chapman and Hall/CRC.
    doi:10.1201/9781003279242
  URL: https://yulab-smu.top/contribution-tree-data/

viridisLite
  License: MIT + file LICENSE
  Citation: Garnier S, Ross N, Rudis R, Camargo AP, Sciaini M, Scherer C
    (2026). viridis(Lite) - Colorblind-Friendly Color Maps for R.
  URL: https://sjmgarnier.github.io/viridis/

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R Package Dependencies (Suggests)
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treeio (>= 1.0)
  License: Artistic-2.0
  Citation: Xu S, Li L, Luo X, Chen M, Tang W, Zhan L, Dai Z, Lam TT,
    Guan Y, Yu G (2022). "Ggtree: A serialized data object for
    visualization of a phylogenetic tree and annotation data." iMeta,
    1(4), e56. doi:10.1002/imt2.56
  URL: https://bioconductor.org/packages/treeio/

phangorn (>= 2.0)
  License: GPL (>= 2)
  Citation: Schliep KP (2011). "phangorn: phylogenetic analysis in R."
    Bioinformatics, 27(4), 592-593. doi:10.1093/bioinformatics/btq706
  URL: https://github.com/KlausVigo/phangorn

RColorBrewer
  License: Apache License 2.0
  Citation: Neuwirth E (2022). RColorBrewer: ColorBrewer Palettes. R
    package.
  URL: https://CRAN.R-project.org/package=RColorBrewer

cowplot (>= 1.1)
  License: MIT + file LICENSE
  URL: https://wilkelab.org/cowplot/

patchwork (>= 1.1)
  License: MIT + file LICENSE
  URL: https://patchwork.data-imaginist.com/

shiny (>= 1.7)
  License: GPL-3
  URL: https://shiny.posit.co/

optparse (>= 1.7)
  License: GPL (>= 2)
  URL: https://CRAN.R-project.org/package=optparse

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Bundled Data
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1. ICS Geological Timescale Data
   File: R/sysdata.rda (compiled from data-raw/make_geo_timescales.R)
   Source: International Commission on Stratigraphy (ICS) International
     Chronostratigraphic Chart, version 2023/02
   URL: https://stratigraphy.org/chart/
   Reference: Gradstein FM, Ogg JG, Schmitz MD, Ogg GM (2020). The
     Geologic Time Scale 2020. Elsevier.
     doi:10.1016/C2020-1-02469-3
   Note: Geological boundary ages are factual data. The color codes
     follow the ICS standard color scheme. The ICS chart is available
     for educational and research use; see
     https://stratigraphy.org/chart/ for terms.

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Standards and Formats Referenced
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- Newick format: https://evolution.genetics.washington.edu/phylip/newicktree.html
- NEXUS format: Maddison DR, Swofford DL, Maddison WP (1997).
  "NEXUS: an extensible file format for systematic information."
  Systematic Biology, 46(4), 590-621. doi:10.1093/sysbio/46.4.590
- GTDB: https://gtdb.ecogenomic.org/
- SILVA: https://www.arb-silva.de/
- NCBI Taxonomy: https://www.ncbi.nlm.nih.gov/taxonomy
- ISO 8601 date/time format: https://en.wikipedia.org/wiki/ISO_8601
