obitaxonomy: manage and query a taxonomy database
#
Description #
obitaxonomy
is the OBITools4 utility for loading, inspecting, and querying a
taxonomy database. It covers every aspect of taxonomy management needed in a metabarcoding
pipeline: downloading a fresh copy of the NCBI taxonomy, exploring the hierarchy, filtering to
a clade of interest, looking up taxon names, and exporting subtrees in CSV or Newick format.
graph LR
T@{ shape: cyl, label: "ncbitaxo.tgz" }
S@{ shape: doc, label: "sequences.fasta" }
C[obitaxonomy]
D@{ shape: doc, label: "taxonomy.csv" }
T --> C
S -. --extract-taxonomy .-> C
C --> D:::data
classDef obitools fill:#99d57c
The command operates in one of several modes depending on the options provided:
| Mode | Trigger | Description |
|---|---|---|
| Name query | positional arguments | Search taxon names by regex (or literal with --fixed). Default mode. |
| Subtree dump | --dump <TAXID> | Output all taxa in the subtree rooted at the given taxid, as CSV or Newick. |
| Lineage | --parents <TAXID> | Print the full ancestral path from a taxid to the taxonomy root. |
| Rank list | --rank-list | List all taxonomic ranks present in the taxonomy. |
| Extract | --extract-taxonomy | Build a local taxonomy from the taxid annotations in a sequence file. |
| Download | --download-ncbi | Fetch the latest NCBI taxonomy dump from the NCBI FTP server. |
Output format #
By default obitaxonomy
writes a CSV table to standard output. Each row represents
one taxon with the following default columns:
| Column | Description |
|---|---|
taxid | Taxon identifier, written as taxon:ID [name]@rank (e.g. taxon:9615 [Canis lupus familiaris]@subspecies). Plain integer with --raw-taxid. |
parent | Parent taxon, also written as taxon:ID [name]@rank. Plain integer with --raw-taxid. |
taxonomic_rank | Taxonomic rank of the taxon (e.g. species, genus, family). |
scientific_name | Scientific name of the taxon. Omit with --without-scientific-name. |
Additional columns:
| Column | Option | Notes |
|---|---|---|
query | --with-query | Inserted as the first column; contains the search query that matched the taxon. |
path | --with-path | Full lineage from the taxon to the root, formatted as ID@name@rank|.... |
Example: single-taxon lookup #
obitaxonomy -t ncbitaxo.tgz --fixed "Canis lupus familiaris" \
| csvlook
| taxid | parent | taxonomic_rank | scientific_name |
| ---------------------------------------------- | -------------------------------- | -------------- | ---------------------- |
| taxon:9615 [Canis lupus familiaris]@subspecies | taxon:9612 [Canis lupus]@species | subspecies | Canis lupus familiaris |
Example: lineage of domestic dog #
obitaxonomy -t ncbitaxo.tgz --parents 9615
| taxid | parent | taxonomic_rank | scientific_name |
| ----------------------------------------------- | ----------------------------------------------- | -------------- | ---------------------- |
| taxon:9615 [Canis lupus familiaris]@subspecies | taxon:9612 [Canis lupus]@species | subspecies | Canis lupus familiaris |
| taxon:9612 [Canis lupus]@species | taxon:9611 [Canis]@genus | species | Canis lupus |
| taxon:9611 [Canis]@genus | taxon:9608 [Canidae]@family | genus | Canis |
| taxon:9608 [Canidae]@family | taxon:379584 [Caniformia]@suborder | family | Canidae |
| taxon:379584 [Caniformia]@suborder | taxon:33554 [Carnivora]@order | suborder | Caniformia |
| taxon:33554 [Carnivora]@order | taxon:314145 [Laurasiatheria]@superorder | order | Carnivora |
| taxon:314145 [Laurasiatheria]@superorder | taxon:1437010 [Boreoeutheria]@clade | superorder | Laurasiatheria |
| taxon:1437010 [Boreoeutheria]@clade | taxon:9347 [Eutheria]@clade | clade | Boreoeutheria |
| taxon:9347 [Eutheria]@clade | taxon:32525 [Theria]@clade | clade | Eutheria |
| taxon:32525 [Theria]@clade | taxon:40674 [Mammalia]@class | clade | Theria |
| taxon:40674 [Mammalia]@class | taxon:32524 [Amniota]@clade | class | Mammalia |
| taxon:32524 [Amniota]@clade | taxon:32523 [Tetrapoda]@clade | clade | Amniota |
| taxon:32523 [Tetrapoda]@clade | taxon:1338369 [Dipnotetrapodomorpha]@clade | clade | Tetrapoda |
| taxon:1338369 [Dipnotetrapodomorpha]@clade | taxon:8287 [Sarcopterygii]@superclass | clade | Dipnotetrapodomorpha |
| taxon:8287 [Sarcopterygii]@superclass | taxon:117571 [Euteleostomi]@clade | superclass | Sarcopterygii |
| taxon:117571 [Euteleostomi]@clade | taxon:117570 [Teleostomi]@clade | clade | Euteleostomi |
| taxon:117570 [Teleostomi]@clade | taxon:7776 [Gnathostomata]@clade | clade | Teleostomi |
| taxon:7776 [Gnathostomata]@clade | taxon:7742 [Vertebrata]@clade | clade | Gnathostomata |
| taxon:7742 [Vertebrata]@clade | taxon:89593 [Craniata]@subphylum | clade | Vertebrata |
| taxon:89593 [Craniata]@subphylum | taxon:7711 [Chordata]@phylum | subphylum | Craniata |
| taxon:7711 [Chordata]@phylum | taxon:33511 [Deuterostomia]@clade | phylum | Chordata |
| taxon:33511 [Deuterostomia]@clade | taxon:33213 [Bilateria]@clade | clade | Deuterostomia |
| taxon:33213 [Bilateria]@clade | taxon:6072 [Eumetazoa]@clade | clade | Bilateria |
| taxon:6072 [Eumetazoa]@clade | taxon:33208 [Metazoa]@kingdom | clade | Eumetazoa |
| taxon:33208 [Metazoa]@kingdom | taxon:33154 [Opisthokonta]@clade | kingdom | Metazoa |
| taxon:33154 [Opisthokonta]@clade | taxon:2759 [Eukaryota]@domain | clade | Opisthokonta |
| taxon:2759 [Eukaryota]@domain | taxon:131567 [cellular organisms]@cellular root | domain | Eukaryota |
| taxon:131567 [cellular organisms]@cellular root | taxon:1 [root]@no rank | cellular root | cellular organisms |
| taxon:1 [root]@no rank | taxon:1 [root]@no rank | no rank | root |
Synopsis #
obitaxonomy [--alternative-names|-a] [--batch-mem <string>]
[--batch-size <int>] [--batch-size-max <int>] [--debug]
[--download-ncbi] [--dump|-D <TAXID>] [--extract-taxonomy]
[--fail-on-taxonomy] [--fixed|-F] [--help|-h|-?]
[--max-cpu <int>] [--newick-output] [--no-progressbar]
[--out|-o <FILENAME>] [--parents|-p <TAXID>] [--pprof]
[--pprof-goroutine <int>] [--pprof-mutex <int>] [--rank <RANK>]
[--rank-list|-l] [--raw-taxid]
[--restrict-to-taxon|-r <string>]... [--silent-warning]
[--solexa] [--sons|-s <TAXID>] [--taxonomy|-t <string>]
[--update-taxid] [--version] [--with-leaves] [--with-path]
[--with-query|-P] [--without-parent] [--without-rank|-R]
[--without-root] [--without-scientific-name|-S] [<args>]
Options #
obitaxonomy specific options #
Data acquisition #
--download-ncbi: Download the current NCBI taxonomy taxdump (default: false)--extract-taxonomy: Extract taxonomy from a sequence file (default: false)--with-leaves: When used with--extract-taxonomy, adds the input sequences themselves as leaf nodes under their respective taxids in the extracted taxonomy. (default: false)
Taxonomy inspection #
--dump|-D<TAXID>: Dump a sub-taxonomy corresponding to the precised clade (default: “”)--newick-output: When used with--dump, writes the taxonomy subtree as a Newick-format tree string instead of the default CSV output. (default: false)--without-root: When used with--newick-output, excludes the non-branching path from the specified clade root up to the overall taxonomy root (taxid 1). Useful for keeping the output focused on the clade of interest. (default: false)--parents|-p<TAXID>: Displays every parental tree’s information for the provided taxid. (default: “NA”)--sons|-s<TAXID>: Displays every sons’ tree’s information for the provided taxid. (default: “NA”)--rank-list|-l: List every taxonomic rank available in the taxonomy. (default: false)
Name queries and filtering #
--fixed: Match taxon names using a fixed pattern, not a regular expression (default: false)--alternative-names|-a: Enable the search on all alternative names and not only scientific names. (default: false)--restrict-to-taxon|-r<string>: Restrict output to some subclades. (default: [])--rank<RANK>: Restrict to the given taxonomic rank. (default: “”)
Output column control #
--with-query|-P: Adds a column containing query used to filter taxon name for each displayed taxon. (default: false)--with-path: Adds a column containing the full path for each displayed taxon. (default: false)--without-scientific-name|-S: Supress the column containing the scientific name from the output. (default: false)--without-rank|-R: Supress the column containing the taxonomic rank from the output. (default: false)--without-parent: Supress the column containing the parent’s taxonid from the output. (default: false)--raw-taxid: Outputs both the taxid and parent columns as plain integer strings, without the taxon:ID [name]@rank formatting. (default: false)
Taxonomy options #
--taxonomy|-t<string>: Path to the taxonomic database.--update-taxid: Automatically replaces taxids that have been declared as merged into a newer taxid in the taxonomy. A warning is emitted for each updated taxid. (default: false)--fail-on-taxonomy: Exits with a fatal error if any taxid encountered during processing is not a currently valid entry in the taxonomy. Combine with--update-taxidto first auto-update deprecated taxids before applying this check. (default: false)
General options #
--help|-h|-?: shows this help.--version: prints the version and exits.--silent-warning: This option tells obitools to stop displaying warnings. This behaviour can be controlled by setting the OBIWARNINGS environment variable.
Computation related options #
--max-cpu<INTEGER>: OBITools can take advantage of your computer’s multi-core architecture by parallelizing the computation across all available CPUs. Computing on more CPUs usually requires more memory to perform the computation. Reducing the number of CPUs used to perform a calculation is also a way to indirectly control the amount of memory used by the process. The number of CPUs used by OBITools can also be controlled by setting the OBIMAXCPU environment variable.--force-one-cpu: forces the use of a single CPU core for parallel processing (default: false).--batch-size<INTEGER>: minimum number of sequences per batch for parallel processing (floor, default: 1, env: OBIBATCHSIZE)--batch-size-max<INTEGER>: maximum number of sequences per batch for parallel processing (ceiling, default: 2000, env: OBIBATCHSIZEMAX)--batch-mem<STRING>: maximum memory per batch (e.g. 128K, 64M, 1G; default: 128M; set to 0 to disable, env: OBIBATCHMEM)
Debug related options #
--debug: enables debug mode, by setting log level to debug (default: false, env: OBIDEBUG)--pprof: enables pprof server. Look at the log for details. (default: false).--pprof-mutex<INTEGER>: enables profiling of mutex lock. (default: 10, env: OBIPPROFMUTEX)--pprof-goroutine<INTEGER>: enables profiling of goroutine blocking profile. (default: 6060, env: OBIPPROFGOROUTINE)
Examples #
Download the NCBI taxonomy #
Fetch the current NCBI taxonomy dump and save it locally:
obitaxonomy --download-ncbi
The output file is named ncbitaxo_YYYYMMDD.tgz (today’s date) by default. You can decide for the filename using the --out option.
obitaxonomy --download-ncbi \
--out ncbitaxo.tgz
List available taxonomic ranks #
Print all taxonomic ranks present in the loaded taxonomy:
obitaxonomy -t ncbitaxo.tgz \
--rank-list \
| csvlook
| rank |
| ---------------- |
| strain |
| kingdom |
| subcohort |
| realm |
| subvariety |
| genus |
| subfamily |
| phylum |
| clade |
| infraorder |
| superorder |
| species subgroup |
| pathogroup |
| species |
| family |
| subclass |
| no rank |
| biotype |
| species group |
| forma |
| parvorder |
| acellular root |
| cellular root |
| tribe |
| class |
| isolate |
| genotype |
| section |
| domain |
| subspecies |
| subphylum |
| superfamily |
| subgenus |
| cohort |
| superphylum |
| subsection |
| order |
| varietas |
| forma specialis |
| superclass |
| serotype |
| subtribe |
| series |
| morph |
| serogroup |
| suborder |
| infraclass |
| subkingdom |
The NCBI taxonomy (version used here) contains 49 distinct taxonomic ranks.
Name query — fixed string #
Search for a taxon using an exact (literal) name match:
obitaxonomy -t ncbitaxo.tgz \
--fixed \
"Canis lupus familiaris" \
| csvlook
| taxid | parent | taxonomic_rank | scientific_name |
| ---------------------------------------------- | -------------------------------- | -------------- | ---------------------- |
| taxon:9615 [Canis lupus familiaris]@subspecies | taxon:9612 [Canis lupus]@species | subspecies | Canis lupus familiaris |
Name query — regular expression pattern with alternative names #
By default, without the --fixed option, the query term is considered a regular expression pattern. To search for all taxa with ‘wolf’ in their name, including synonyms and common names, use the --alternative-names option. Adding the --with-query option displays the query as the first column.
obitaxonomy -t ncbitaxo.tgz \
--alternative-names \
--with-query \
"wolf" \
| csvlook
| query | taxid | parent | taxonomic_rank | scientific_name |
| ----- | ------------------------------------------------------------------ | ---------------------------------------------------- | -------------- | ---------------------------------- |
| wolf | taxon:3374999 [Klebsiella phage vB_KpnM_Wolf_ER13]@species | taxon:12333 [unclassified bacterial viruses]@no rank | species | Klebsiella phage vB_KpnM_Wolf_ER13 |
| wolf | taxon:2913901 [Meteora]@genus | taxon:2683617 [Eukaryota incertae sedis]@no rank | genus | Meteora |
| wolf | taxon:2942894 [Microwolfvirus]@genus | taxon:2731619 [Caudoviricetes]@class | genus | Microwolfvirus |
| wolf | taxon:1034136 [Microwolfvirus JHC117]@species | taxon:2942894 [Microwolfvirus]@genus | species | Microwolfvirus JHC117 |
| wolf | taxon:2956194 [Microwolfvirus zetzy]@species | taxon:2942894 [Microwolfvirus]@genus | species | Microwolfvirus zetzy |
| ... | ... | ... | ... | ... |
This query returns 736 rows including all taxa whose scientific name or any alternative name contains the word “wolf”.
Dump a clade — species only #
Output all species in the order Carnivora (taxid 33554):
obitaxonomy -t ncbitaxo.tgz \
--dump 33554 \
--rank species \
| csvlook
| taxid | parent | taxonomic_rank | scientific_name |
| ------------------------------------------------- | ----------------------------------------------- | -------------- | ---------------------------- |
| taxon:2828883 [Ursus kanivetz]@species | taxon:9639 [Ursus]@genus | species | Ursus kanivetz |
| taxon:1825730 [Arctotherium sp.]@species | taxon:2640560 [unclassified Arctotherium]@no rank | species | Arctotherium sp. |
| taxon:816549 [Carnivora sp. BOLD:AAF4913]@species | taxon:727684 [unclassified Carnivora]@no rank | species | Carnivora sp. BOLD:AAF4913 |
| taxon:9644 [Ursus arctos]@species | taxon:9639 [Ursus]@genus | species | Ursus arctos |
| ... | ... | ... | ... |
This returns 418 species. Without --rank species, the full Carnivora subtree (all ranks) is returned. If the --without-root option is not selected, the output will also include the taxonomic path from Carnivora up to the root (taxid 1).
Extract taxonomy from a sequence file #
Build a local taxonomy from the taxid annotations embedded in a sequence file, including the sequence entries themselves as leaf nodes:
obitaxonomy -t ncbitaxo.tgz \
--extract-taxonomy \
--with-leaves \
db_v05_r117.fasta.gz \
> taxo_db_v05_r117.csv
Below the first ten lines of the taxo_db_v05_r117.csv
csvlook taxo_db_v05_r117.csv \
| head
| taxid | parent | taxonomic_rank | scientific_name |
| -------------------------------------------------------------------------- | ------------------------------------------------------------------ | -------------- | -------------------------------------------------- |
| taxon:1 [root]@no rank | taxon:1 [root]@no rank | no rank | root |
| taxon:131567 [cellular organisms]@cellular root | taxon:1 [root]@no rank | cellular root | cellular organisms |
| taxon:2759 [Eukaryota]@domain | taxon:131567 [cellular organisms]@cellular root | domain | Eukaryota |
| taxon:33154 [Opisthokonta]@clade | taxon:2759 [Eukaryota]@domain | clade | Opisthokonta |
| taxon:33208 [Metazoa]@kingdom | taxon:33154 [Opisthokonta]@clade | kingdom | Metazoa |
| taxon:6072 [Eumetazoa]@clade | taxon:33208 [Metazoa]@kingdom | clade | Eumetazoa |
| taxon:6073 [Cnidaria]@phylum | taxon:6072 [Eumetazoa]@clade | phylum | Cnidaria |
| taxon:6142 [Scyphozoa]@class | taxon:6073 [Cnidaria]@phylum | class | Scyphozoa |
This returns 13 815 taxonomy nodes
- the 9 605 unique taxids referenced in the file,
- their ancestors up to the root,
- plus the sequences themselves added as leaves.
If you only want simple taxid without any supplementary information, you can add the --raw-taxid option.
obitaxonomy -t ncbitaxo.tgz \
--extract-taxonomy \
--raw-taxid \
db_v05_r117.fasta.gz \
> taxo_db_v05_r117_raw.csv
csvlook taxo_db_v05_r117_raw.csv \
| head
| taxid | parent | taxonomic_rank | scientific_name |
| --------- | --------- | -------------- | -------------------------------------------------- |
| 1 | 1 | no rank | root |
| 131,567 | 1 | cellular root | cellular organisms |
| 2,759 | 131,567 | domain | Eukaryota |
| 33,154 | 2,759 | clade | Opisthokonta |
| 33,208 | 33,154 | kingdom | Metazoa |
| 6,072 | 33,208 | clade | Eumetazoa |
| 6,073 | 6,072 | phylum | Cnidaria |
| 6,142 | 6,073 | class | Scyphozoa |
Producing a taxonomic tree corresponding to a sequence file #
obitaxonomy -t ncbitaxo.tgz \
--extract-taxonomy \
--newick-output \
--without-root \
out_ecotag.fasta \
> out_ecotag.nwk
produces the following Newick file
📄 out_ecotag.nwk(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
Canis lupus familiaris -9615@subspecies-:1.00000
)Canis lupus -9612@species-:1.00000
)Canis -9611@genus-:1.00000
)Canidae -9608@family-:1.00000
)Caniformia -379584@suborder-:1.00000
)Carnivora -33554@order-:1.00000,
(
(
(
(
(
(
Capreolus capreolus -9858@species-:1.00000
)Capreolus -9857@genus-:1.00000
)Odocoileinae -9881@subfamily-:1.00000,
(
(
Cervus elaphus -9860@species-:1.00000
)Cervus -9859@genus-:1.00000
)Cervinae -34878@subfamily-:1.00000
)Cervidae -9850@family-:1.00000
)Pecora -35500@infraorder-:1.00000
)Ruminantia -9845@suborder-:1.00000
)Artiodactyla -91561@order-:1.00000
)Laurasiatheria -314145@superorder-:1.00000,
(
(
(
(
(
(
(
Marmota -9992@genus-:1.00000
)Marmotini -337730@tribe-:1.00000
)Xerinae -337726@subfamily-:1.00000
)Sciuridae -55153@family-:1.00000
)Sciuromorpha -33553@suborder-:1.00000
)Rodentia -9989@order-:1.00000
)Glires -314147@clade-:1.00000
)Euarchontoglires -314146@superorder-:1.00000
)Boreoeutheria -1437010@clade-:1.00000
)Eutheria -9347@clade-:1.00000
)Theria -32525@clade-:1.00000
)Mammalia -40674@class-:1.00000
)Amniota -32524@clade-:1.00000
)Tetrapoda -32523@clade-:1.00000
)Dipnotetrapodomorpha -1338369@clade-:1.00000
)Sarcopterygii -8287@superclass-:1.00000
)Euteleostomi -117571@clade-:1.00000
)Teleostomi -117570@clade-:1.00000
)Gnathostomata -7776@clade-:1.00000
)Vertebrata -7742@clade-:1.00000
)Craniata -89593@subphylum-:1.00000
)Chordata -7711@phylum-:1.00000
)Deuterostomia -33511@clade-:1.00000
)Bilateria -33213@clade-:1.00000
)Eumetazoa -6072@clade-:1.00000
)Metazoa -33208@kingdom-:1.00000
)Opisthokonta -33154@clade-:1.00000
)Eukaryota -2759@domain-:1.00000
)cellular organisms -131567@cellular root-:1.00000
)root -1@no rank-;
That can be displayed as the following tree:
Loading tree…
Filter by clade and rank — with full lineage path #
List all genera within the family Bovidae (taxid 9895), showing the full taxonomic path but
hiding the parent column:
obitaxonomy -t ncbitaxo.tgz \
--restrict-to-taxon 9895 \
--rank genus \
--with-path \
--without-parent \
| csvlook
| taxid | taxonomic_rank | scientific_name | path |
| ----------------------------------- | -------------- | --------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| taxon:3026943 [Cephalophorus]@genus | genus | Cephalophorus | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9952@Cephalophinae@subfamily|3026943@Cephalophorus@genus |
| taxon:59514 [Addax]@genus | genus | Addax | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9959@Hippotraginae@subfamily|59514@Addax@genus |
| taxon:9957 [Oryx]@genus | genus | Oryx | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9959@Hippotraginae@subfamily|9957@Oryx@genus |
| taxon:9954 [Cephalophus]@genus | genus | Cephalophus | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9952@Cephalophinae@subfamily|9954@Cephalophus@genus |
| taxon:119561 [Sylvicapra]@genus | genus | Sylvicapra | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9952@Cephalophinae@subfamily|119561@Sylvicapra@genus |
| taxon:3033999 [Cephalophula]@genus | genus | Cephalophula | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9952@Cephalophinae@subfamily|3033999@Cephalophula@genus |
| taxon:1922214 [Bootherium]@genus | genus | Bootherium | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9963@Caprinae@subfamily|1922214@Bootherium@genus |
| taxon:59516 [Alcelaphus]@genus | genus | Alcelaphus | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|37170@Alcelaphinae@subfamily|59516@Alcelaphus@genus |
| taxon:34874 [Saiga]@genus | genus | Saiga | 1@root@no rank|131567@cellular organisms@cellular root|2759@Eukaryota@domain|33154@Opisthokonta@clade|33208@Metazoa@kingdom|6072@Eumetazoa@clade|33213@Bilateria@clade|33511@Deuterostomia@clade|7711@Chordata@phylum|89593@Craniata@subphylum|7742@Vertebrata@clade|7776@Gnathostomata@clade|117570@Teleostomi@clade|117571@Euteleostomi@clade|8287@Sarcopterygii@superclass|1338369@Dipnotetrapodomorpha@clade|32523@Tetrapoda@clade|32524@Amniota@clade|40674@Mammalia@class|32525@Theria@clade|9347@Eutheria@clade|1437010@Boreoeutheria@clade|314145@Laurasiatheria@superorder|91561@Artiodactyla@order|9845@Ruminantia@suborder|35500@Pecora@infraorder|9895@Bovidae@family|9948@Antilopinae@subfamily|34874@Saiga@genus |
...
The path column contains the full lineage from root to the taxon, with each node encoded as
ID@name@rank and nodes separated by |. This query returns 57 genera.
This returns 1 153 plain integer taxids — the full Primate subtree plus the path to the
taxonomy root. The --raw-taxid flag makes both taxid and parent plain integers instead of the default taxon:ID [name]@rank strings.
obitaxonomy help #
obitaxonomy --help