Galaxy |

ETE lineage generator (version 3.1.2+galaxy1)

Species file:

List with one species/taxid per line

(ETE3) Taxonomy Database:

The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)

Taxonomic levels:

Taxonomic levels to include in the output

Fill unnamed ranks:

Fill unnamed ranks with super/sub ranks (see -l)

Prefer lower ranks:

Take the next available lower rank (default: higher)

Include taxid in the table:

For the case when the input consists of taxon names

Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the ETE Toolkit.

Input

Species file a single column tabular file
(ETE3) Taxonomy Database a sqlite database that has been created by ETE from the NCBI taxonomy dump

Options

Taxonomic levels the columns to be incuded in the output table. There are two presets (full and primary)
- Full contains all 29 ranks included in the NCBI taxonomy
- Primary contains the primary ranks (kingdom, phylum, class, order, family, genus, species)
- Manual the ranks of interest can be chosen by the user. The primary levels are chosen by default.
Fill unnamed ranks Get missing data from "nearby" levels:
- Some nodes in the NCBI taxonomy tree have no name (no rank) these are shown by default as "NA" in the output. If the compress option is selected then the rank is accepted if the level name is included (e.g. superorder is accepted as order if the order is unnamed but the name of the superorder is given)
Prefer lower ranks for filling for compressing lower levels are prefered over higher ones

Output

Table (tab separated). The first column contains the species names. The following columns contain the rank names of the levels of interest.