Package: Rclade 1.1.5

Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

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) <doi:10.1111/2041-210X.12628>, 'deeptime' Gearty (2025) <doi:10.1080/20964471.2025.2537516>, and 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633>.

Authors:Zeng Zichao [aut, cre]

Rclade_1.1.5.tar.gz
Rclade_1.1.5.zip(r-4.7-any)Rclade_1.1.5.zip(r-4.6-any)Rclade_1.1.5.zip(r-4.5-any)
Rclade_1.1.5.tgz(r-4.6-any)Rclade_1.1.5.tgz(r-4.5-any)
Rclade_1.1.5.tar.gz(r-4.7-any)Rclade_1.1.5.tar.gz(r-4.6-any)
Rclade_1.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rclade/json (API)

# Install 'Rclade' in R:
install.packages('Rclade', repos = c('https://zengzichao.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zengzichao/rclade/issues

Pkgdown/docs site:https://zengzichao.github.io

Datasets:

On CRAN:

Conda:

bioinformaticsdata-visualizationdeeptimeggtreephylogenetic-treephylogeneticstaxonomy

5.32 score 2 stars 158 downloads 26 exports 91 dependencies

Last updated from:9a1a6288be. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK217
source / vignettesOK406
linux-releaseOK217
macos-releaseOK133
macos-oldrelOK130
windows-develOK136
windows-releaseOK142
windows-oldrelOK145
wasm-releaseOK150

Exports:batch_plotcheck_monophylycheck_special_monophylydetect_taxonomy_formatget_supported_extensionsparse_taxonomyplot_timetreerclade_logorclade_optionsread_taxonomy_fileread_tree_autorun_rclade_clirun_rclade_selftestrun_rclade_shinysave_session_infosave_timetreeset_log_enabledset_log_fileset_log_levelsummarize_taxonomy_qualitysummarize_taxonomy_quality_with_filesummarize_timetreetheme_timetreevalidate_sequence_deepvalidate_sequence_filevalidate_tree_sequence_match

Dependencies:apeaplotbase64encbslibcachemclicommonmarkcpp11curldeeptimedeeptimedatadigestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggfittextggforceggfunggh4xggiraphggplot2ggplotifyggtreegluegridExtragridGraphicsgridtextgrImport2gtablehighrhtmltoolshtmlwidgetsisobandjpegjquerylibjsonliteknitrlabelinglatticelazyevallifecyclelitedownmagrittrmarkdownMASSmemoisemimenlmepatchworkpillarpkgconfigpngpolyclippurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesshadesstringistringrsystemfontstibbletidyrtidyselecttidytreetinytextreeiotweenrutf8vctrsviridisLitewithrxfunXMLxml2yamlyulab.utils

Quick Start: From Tree File to Publication Figure
Installation | Basic Usage | Adding Titles | Summarizing Results | Saving Output | Taxonomy Quality Check | References & Acknowledgments
Rendered fromquick_start.Rmdusingknitr::rmarkdown

Last update: 2026-08-26
Started: 2026-08-13

Supported Taxonomy Label Formats
Overview | Automatic Detection | Quality Report | Manual Format Specification | NCBI Format Handling | Custom Regex Patterns | Embedded Format Parsing Strategies | Custom Taxonomy Levels | References & Acknowledgments
Rendered fromtaxonomy_formats.Rmdusingknitr::rmarkdown

Last update: 2026-08-26
Started: 2026-08-13

Publication-Ready Output
Color-Blind Friendly Palettes | Custom Color Mapping | Legend Placement | Clade Labels | Taxonomy Quality Report | Batch Processing | Reproducibility | References & Acknowledgments
Rendered frompublication_ready.Rmdusingknitr::rmarkdown

Last update: 2026-08-21
Started: 2026-08-13

Readme and manuals

Help Manual

Help pageTopics
Batch plot timetrees from a directory of tree filesbatch_plot
Check if a taxonomic group is monophyleticcheck_monophyly
Check if a special identifier corresponds to a monophyletic groupcheck_special_monophyly
Detect taxonomy format from tip labelsdetect_taxonomy_format
Example phylogenetic tree with GTDB-style labelsexample_tree
Get supported file extensionsget_supported_extensions
Unified taxonomy parsing entry pointparse_taxonomy
Plot a phylogenetic tree with geological timescale and taxonomic collapsingplot_timetree
Example phylogenetic tree with polytomiespolytomy_tree
Display Rclade ASCII art logorclade_logo
Construct a validated options list for 'plot_timetree()'rclade_options
Read taxonomy information from a table fileread_taxonomy_file
Read tree from file with automatic format detectionread_tree_auto
Run Rclade from the command linerun_rclade_cli
Run Rclade self-testrun_rclade_selftest
Launch Rclade Shiny apprun_rclade_shiny
Save sessionInfo() for reproducibilitysave_session_info
Save a timetree plot to filesave_timetree
Enable or disable loggingset_log_enabled
Set log file for dual outputset_log_file
Set log levelset_log_level
Report taxonomy label parsing qualitysummarize_taxonomy_quality
Summarize taxonomy quality with external file supportsummarize_taxonomy_quality_with_file
Print a summary of a Rclade timetree plotsummarize_timetree
Publication-ready theme for timetree plotstheme_timetree
Deep validation of sequence filesvalidate_sequence_deep
Validate sequence file formatvalidate_sequence_file
Cross-validate tree tip labels against sequence IDsvalidate_tree_sequence_match