Parc
Open tree, alignment and downloads · Sequence extraction result
Ref NR99
Open tree, alignment and downloads · Sequence extraction result
Server: yurai (CGI)
Tree Identification (Fungi) · Sequence Extraction (Fungi)
5 October 2026 · Public beta testing
Same 27 decaying-wood eDNA OTUs (Shirouzu et al. 2020, Figs. 2 and 3 ; Matsuoka 2022, p. 221, Fig. 3). Tree settings: first 10 queries; 20 reference hits per query; up to 150 anonymous hits; E-value 1e-3; minimum 80% identity and 70% query coverage; MAFFT, trimAl, NJ TN93, 100 bootstrap replicates. The per-OTU table below separately searches all 27 sequences under the same BLAST settings.
Initial LSU database: Parc. For this example, Parc retains closer references for all 27 OTUs. This does not establish that Parc is preferable for every organism or marker region. Higher BLAST identity does not by itself establish species identity.
| Measure | Parc | Ref NR99 |
|---|---|---|
| Reference sequences | 1312521 | 95279 |
| Queries with qualifying hits | 27 | 27 |
| Best-hit identity range (%) | 94.613–100.000 | 85.668–95.410 |
| Tree tips | 145 | 103 |
| Retained alignment sites | 258 | 305 |
| Tree pipeline seconds (single stage run; not a benchmark) | 12.8 | 4.89 |
| Extraction keyword Dacrymycetes: matching records | 191 | 1 |
Taxonomy is retained from SILVA. Some lineages disagree with submitted organism names: LC003982.1.611 is placed in Agaricomycetes / Serpulaceae / Serpula, but is named “uncultured Dacrymycetes”. MH877696.1.855 is placed in Tremellomycetes / Tremellales, but is named “Ditiola nuda”. The extraction counts above are literal keyword matches, not independently verified class membership. Missing family ranks are shown as unclassified.
No example accessions were removed from SILVA. This is a comparison of database choices, not an independent validation. The source paper used RAxML; these NJ trees do not reproduce its inference method.
Open tree, alignment and downloads · Sequence extraction result
Open tree, alignment and downloads · Sequence extraction result
One hit is shown when scores tie; names below are database organism labels, not species assignments. Download comparison TSV
| OTU | Parc organism label | Identity / coverage (%) | Ref NR99 organism label | Identity / coverage (%) |
|---|---|---|---|---|
| OTU_3 | Dacrymyces australis | 100.0 / 100.0 | Dacrymyces stillatus | 95.238 / 86.897 |
| OTU_29 | uncultured Dacrymycetes | 98.969 / 100.0 | Ramaria stricta | 85.668 / 100.0 |
| OTU_96 | Dacrymycetes sp. | 99.31 / 98.639 | Trechispora farinacea | 86.557 / 100.0 |
| OTU_97 | Ditiola nuda | 97.241 / 100.0 | Dacrymyces stillatus | 92.063 / 86.897 |
| OTU_103 | Dacrymyces lacrymalis | 100.0 / 96.552 | Dacrymyces stillatus | 92.46 / 86.897 |
| OTU_120 | uncultured Dacrymycetes | 98.276 / 100.0 | Dacrymyces stillatus | 92.063 / 86.897 |
| OTU_155 | Dacrymyces variisporus | 96.587 / 96.7 | Phaffia rhodozyma | 90.909 / 100.0 |
| OTU_177 | Dacrymyces capitatus | 98.625 / 100.0 | Dacrymyces stillatus | 92.063 / 86.897 |
| OTU_194 | uncultured Dacrymycetes | 98.621 / 100.0 | Dacrymyces stillatus | 92.46 / 86.897 |
| OTU_196 | Dacrymyces variisporus | 100.0 / 96.7 | Phaffia rhodozyma | 88.312 / 100.0 |
| OTU_211 | Dacrymyces minutus | 95.088 / 95.946 | Mrakia blollopis | 88.925 / 100.0 |
| OTU_214 | Dacrymycetes sp. NBRC 110597 | 100.0 / 96.026 | Botryobasidium subcoronatum | 94.426 / 100.0 |
| OTU_228 | Dacryoscyphus chrysochilus | 98.233 / 97.586 | Dacrymyces stillatus | 90.476 / 86.897 |
| OTU_241 | Dacrymycetes sp. 7 ST-2014 | 100.0 / 96.04 | Phaffia rhodozyma | 91.558 / 100.0 |
| OTU_248 | uncultured Dacrymycetes | 100.0 / 100.0 | Dacrymyces stillatus | 92.857 / 86.897 |
| OTU_258 | uncultured Dacrymycetes | 99.661 / 100.0 | Ramaria stricta | 88.026 / 100.0 |
| OTU_263 | uncultured Dacrymycetes | 99.322 / 100.0 | Ramaria stricta | 87.013 / 100.0 |
| OTU_266 | Ceratobasidium pseudocornigerum | 99.333 / 99.01 | Fomitopsis palustris | 95.41 / 100.0 |
| OTU_272 | uncultured Dacrymycetes | 100.0 / 100.0 | Botryobasidium subcoronatum | 94.098 / 100.0 |
| OTU_278 | Dacrymyces citrinus | 98.535 / 91.919 | Phellinus noxius OVT-YTM/97 | 89.508 / 100.0 |
| OTU_323 | Dacrymyces minutus | 95.122 / 95.96 | Trechispora farinacea | 89.508 / 100.0 |
| OTU_345 | uncultured Dacrymycetes | 95.593 / 100.0 | Ramaria stricta | 87.948 / 100.0 |
| OTU_356 | uncultured Dacrymycetes | 99.317 / 100.0 | Sarcomyxa serotina | 85.668 / 98.976 |
| OTU_367 | Cerinosterus luteoalbus | 94.613 / 100.0 | Mrakia blollopis | 89.251 / 100.0 |
| OTU_466 | uncultured Dacrymycetes | 97.627 / 100.0 | Ramaria stricta | 86.319 / 100.0 |
| OTU_494 | uncultured Dacrymycetes | 100.0 / 100.0 | Dacrymyces stillatus | 93.651 / 86.897 |
| OTU_495 | Femsjonia uniseptata | 100.0 / 100.0 | Mrakia blollopis | 88.925 / 100.0 |
SILVA 138.2 documentation · SILVA attribution and CC BY 4.0 license · Example source paper