Supported Taxonomy Label Formats

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Overview

Rclade automatically detects and parses four taxonomy label formats:

Format	Separator	Prefix	Example
GTDB	`;`	`__`	`d__Bacteria;p__Proteobacteria`
Silva	`;`	none	`Bacteria;Proteobacteria`
NCBI	`;`	none	`cellular organisms;Bacteria`
Custom rank	`_` + code	none	`species_d_Bacteria_p_Proteobacteria`

Automatic Detection

library(Rclade)

# Load example data
data(example_tree)

# Auto-detection works in most cases
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "auto",
                   add_timescale = FALSE)
#> 
#> ============================================================
#>            Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:28.155+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-09-16T00:09:28.155+08:00 | INFO     | Tree input               : phylo object
#> 2026-09-16T00:09:28.155+08:00 | INFO     | Rank                     : phylum
#> 2026-09-16T00:09:28.155+08:00 | INFO     | Layout                   : rectangular
#> 2026-09-16T00:09:28.155+08:00 | INFO     | Unit                     : auto
#> 2026-09-16T00:09:28.155+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-09-16T00:09:28.156+08:00 | INFO     | Tips                     : 50
#> 2026-09-16T00:09:28.156+08:00 | INFO     | Internal nodes           : 49
#> 2026-09-16T00:09:28.156+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-09-16T00:09:28.156+08:00 | INFO     | Input validation passed
#> 2026-09-16T00:09:28.157+08:00 | INFO     | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:28.157+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:28.157+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:28.160+08:00 | INFO     | Detected format          : GTDB
#> 2026-09-16T00:09:28.161+08:00 | INFO     | Groups found             : 5
#> 2026-09-16T00:09:28.161+08:00 | INFO     | Timer 'taxonomy_parsing': 4 ms
#> 2026-09-16T00:09:28.161+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:28.161+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:28.162+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:28.162+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-09-16T00:09:28.163+08:00 | INFO     | Timer 'mrca_computation': 1 ms
#> 2026-09-16T00:09:28.163+08:00 | INFO     | Step 4/7: Color generation
#> 2026-09-16T00:09:28.163+08:00 | INFO     | Color palette            : viridis
#> 2026-09-16T00:09:28.163+08:00 | INFO     | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:28.205+08:00 | INFO     | Collapsing 5 clades...
#> 2026-09-16T00:09:28.216+08:00 | INFO     | Clade collapse complete
#> 2026-09-16T00:09:28.216+08:00 | INFO     | Timer 'tree_rendering': 53 ms
#> 2026-09-16T00:09:28.217+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:28.245+08:00 | INFO     |   Tips                        : 50
#> 2026-09-16T00:09:28.245+08:00 | INFO     |   Groups parsed               : 5
#> 2026-09-16T00:09:28.245+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-09-16T00:09:28.246+08:00 | INFO     |   Singleton groups            : 0
#> 2026-09-16T00:09:28.246+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-09-16T00:09:28.246+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-09-16T00:09:28.246+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-09-16T00:09:28.246+08:00 | INFO     |   Layout                      : rectangular
#> 2026-09-16T00:09:28.246+08:00 | INFO     |   Timescale                   : disabled
#> 2026-09-16T00:09:28.246+08:00 | INFO     | plot_timetree completed successfully

Detection applies conservative “clear majority” rules: GTDB requires a [dpcofgsk]__ prefix-match score >= 0.6 and a semicolon-delimiter majority; embedded requires a _[dpcofgsk]_ match score >= 0.6; NCBI/Silva first require a semicolon majority and then compare prefix scores. Ambiguous labels fall back to "unknown". Note that accession-prefixed embedded labels with double-underscore separators (e.g. GCA_xxx_d__Archaea_p__Nanoarchaeota) are correctly detected as embedded (not GTDB) and are parsed by all three delimiter modes; for label schemes with extra intermediate ranks (e.g. a superphylum field), use taxonomy_format = "custom_regex" with explicit per-rank patterns.

Quality Report

Check how well your labels can be parsed before visualization:

labels <- example_tree$tip.label
summarize_taxonomy_quality(labels, format = "GTDB")
#> === Taxonomy Label Parsing Quality Report ===
#> Total labels: 50
#> Detected format: GTDB
#> 
#> Per-rank parse rates:
#>   kingdom        0.0% (0/50) 
#>   domain       100.0% (50/50) ====================
#>   phylum       100.0% (50/50) ====================
#>   class        100.0% (50/50) ====================
#>   order          0.0% (0/50) 
#>   family         0.0% (0/50) 
#>   genus          0.0% (0/50) 
#>   species        0.0% (0/50) 
#>   subspecies     0.0% (0/50) 
#> 
#> All labels parsed successfully.

Manual Format Specification

If auto-detection fails, specify the format explicitly:

# GTDB format
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE)
#> 
#> ============================================================
#>            Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:28.309+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-09-16T00:09:28.309+08:00 | INFO     | Tree input               : phylo object
#> 2026-09-16T00:09:28.309+08:00 | INFO     | Rank                     : phylum
#> 2026-09-16T00:09:28.309+08:00 | INFO     | Layout                   : rectangular
#> 2026-09-16T00:09:28.309+08:00 | INFO     | Unit                     : auto
#> 2026-09-16T00:09:28.310+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-09-16T00:09:28.310+08:00 | INFO     | Tips                     : 50
#> 2026-09-16T00:09:28.310+08:00 | INFO     | Internal nodes           : 49
#> 2026-09-16T00:09:28.310+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-09-16T00:09:28.310+08:00 | INFO     | Input validation passed
#> 2026-09-16T00:09:28.311+08:00 | INFO     | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:28.311+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:28.311+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:28.315+08:00 | INFO     | Detected format          : GTDB
#> 2026-09-16T00:09:28.315+08:00 | INFO     | Groups found             : 5
#> 2026-09-16T00:09:28.315+08:00 | INFO     | Timer 'taxonomy_parsing': 4 ms
#> 2026-09-16T00:09:28.315+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:28.315+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:28.316+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:28.316+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-09-16T00:09:28.317+08:00 | INFO     | Timer 'mrca_computation': 1 ms
#> 2026-09-16T00:09:28.317+08:00 | INFO     | Step 4/7: Color generation
#> 2026-09-16T00:09:28.317+08:00 | INFO     | Color palette            : viridis
#> 2026-09-16T00:09:28.317+08:00 | INFO     | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:28.358+08:00 | INFO     | Collapsing 5 clades...
#> 2026-09-16T00:09:28.370+08:00 | INFO     | Clade collapse complete
#> 2026-09-16T00:09:28.370+08:00 | INFO     | Timer 'tree_rendering': 53 ms
#> 2026-09-16T00:09:28.370+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:28.400+08:00 | INFO     |   Tips                        : 50
#> 2026-09-16T00:09:28.400+08:00 | INFO     |   Groups parsed               : 5
#> 2026-09-16T00:09:28.400+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-09-16T00:09:28.400+08:00 | INFO     |   Singleton groups            : 0
#> 2026-09-16T00:09:28.400+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-09-16T00:09:28.401+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-09-16T00:09:28.401+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-09-16T00:09:28.401+08:00 | INFO     |   Layout                      : rectangular
#> 2026-09-16T00:09:28.401+08:00 | INFO     |   Timescale                   : disabled
#> 2026-09-16T00:09:28.401+08:00 | INFO     | plot_timetree completed successfully
print(p)

NCBI Format Handling

NCBI taxonomy uses position-based rank mapping. Note that this may produce systematic rank offsets in non-standard lineages (e.g., viruses where Riboviria is a realm, not a domain). For critical applications, consider using GTDB or Silva format, or providing custom_patterns.

# NCBI format (requires NCBI-labeled tree)
p <- plot_timetree(ncbi_tree, rank = "phylum",
                   taxonomy_format = "NCBI",
                   add_timescale = FALSE)

Custom Regex Patterns

For non-standard formats:

p <- plot_timetree(tree, rank = "phylum",
                   add_timescale = FALSE,
                   taxonomy_format = "custom_regex",
                   custom_patterns = list(
                     domain = "Domain:([^|]+)",
                     phylum = "Phylum:([^|]+)"
                   ))

Embedded Format Parsing Strategies

For embedded (Format A) labels, Rclade supports three delimiter matching strategies:

Mode	Description	Best for
`reverse` (default)	Match ranks from right to left	Labels where taxon names contain underscores
`greedy`	Match ranks from left to right using character-class boundaries	Simple labels with no underscores in names
`segment`	Extract content between delimiters	Preserving underscores within values

# Default reverse mode
p <- plot_timetree(tree, rank = "phylum",
                   add_timescale = FALSE,
                   taxonomy_format = "custom_rank",
                   taxonomy_delimiter_mode = "reverse")

# Segment mode for labels with underscores in taxon names
p <- plot_timetree(tree, rank = "phylum",
                   add_timescale = FALSE,
                   taxonomy_format = "custom_rank",
                   taxonomy_delimiter_mode = "segment")

Custom Taxonomy Levels

You can extend or override the default rank codes and delimiters with taxonomy_levels. This is useful for non-standard ranks such as kingdom (k) or subspecies (ss).

For embedded (Format A) labels, provide a list of rank codes and their prefixes:

p <- plot_timetree(tree, rank = "phylum",
                   add_timescale = FALSE,
                   taxonomy_format = "custom_rank",
                   taxonomy_levels = list(
                     codes = c("k", "d", "p", "c", "o", "f", "g", "s", "ss"),
                     names = c("_k_", "_d_", "_p_", "_c_",
                               "_o_", "_f_", "_g_", "_s_", "_ss_")
                   ))

The codes vector defines the short rank codes, and names defines the delimiters used in the labels. The same taxonomy_levels object is propagated through highlighting, monophyly checks, special identifier resolution, and external taxonomy file merging.

References & Acknowledgments

Rclade supports taxonomy formats from several databases. If you use data from these sources in published research, please cite them appropriately:

GTDB: Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P (2020). “A complete domain-to-species taxonomy for Bacteria and Archaea.” Nature Biotechnology, 38(9), 1079-1086. doi:10.1038/s41587-020-0501-8
SILVA: Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013). “The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.” Nucleic Acids Research, 41(D1), D590-D596. doi:10.1093/nar/gks1219
NCBI Taxonomy: Sayers EW, et al. (2022). “Database resources of the National Center for Biotechnology Information.” Nucleic Acids Research, 50(D1), D20-D26. doi:10.1093/nar/gkab1112

Rclade also builds on the ggtree and deeptime R packages:

Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees.” Methods in Ecology and Evolution, 8(1), 28-36. doi:10.1111/2041-210X.12628
Gearty W (2025). “deeptime: an R package for visualizations of data over geological time intervals.” Big Earth Data. doi:10.1080/20964471.2025.2537516

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They may not be fully stable and should be used with caution. We make no claims about them.
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