ecofind: querying a taxonomic database

ecofind retrive taxonomic information from taxonomic database given either a taxid or a regular expression patterns.

ecofind specific options

-d <filename>

Filename containing the database used for the in silico PCR. The database must be in the ecoPCR format (see obiconvert).


This option is compulsory.


Enable the search on all alternative names and not only scientific names.


List all taxonomic rank available for -r option and exit.


Restrict to given taxonomic rank.


Displays all subtree’s information for the given taxid.


Displays all parental tree’s information for the given taxid.


Display taxonomic Path as suplementary column in output


Print help.

Output file

The output file contains several columns, with ‘|’ as separator, and describes the properties of the retrieved taxids.

column 1: the taxid

column 2: the taxonomic rank

column 3: the name (not only scientific)

column 4: class name

column 5: the scientific name

column 6 (optional): the full taxonomic path of the taxid


Example 1:

>  ecofind -d mydatabase 'homo ' >

Retrieve all taxids whose ‘homo ‘ is contained in the associated names.

Example 2:

> ecofind -d mydatabase  -p 9606 -P >

Retrieve all parents taxa of the 9606 taxid. The -P option add a supplementary column with the full path for each taxid.