Advanced mode: Submit your query

xleBIBI has allowed the phylogenetic positioning of unknown prokaryotes since 2002 with two major modifications in 2015 and this version since 2021.
THIS TOOL MAY BE STOPPED AT ANY MOMENT NOW due to acute safety concern.

PkXplore has been developped for teaching purposes but may be a partial alternative

Query Format

Format must be FASTA: >your_description
ATGCATGC... the nucleic sequence (16S, 23S will hopefully come soon)

OR #Genus_species :

for exemple #Methanothermus_sociabilis, Note that BLAST may not return all relevant sequences.

Paste the query here (or ? or help) then proceed to the next step

DB choice

The default DB is the "16S Prototypes sequences low redundancy" containing one to a few sequence per species. These sequences are selected on their quality and representativity.

DB linked to riboDB : : DNA-directed-RNA-polymerase subunit beta and beta/beta' DB (Type strains or best representative). Be aware of the presence of more that one sequence of the protein in some genomes.
This DB has the lower redundancy possible as its construction follows the same rules used in Prototypes sequences low redundancy 16S DB

Other DB

the very old Corynebacteriales-Chaperonine-groEL DB is available but its integration in the results pages may not be optimal.

DB choice:

Parameters

The default number if sequences is 100, you may increase it up to 400

Number of recruited sequences

The default ALIGNER is kalign

Select a new aligner

The default trimming tool is only removing columns with more than 45% gaps

Select a new trimming tool

Trying to mitigate low quality positions of the query is the default
(mitigation not available if Gblocks is the trimmer)

Select the mitigation

Polytomy when nodes SH level under 0.2 is the default

Select the level for polytomy

Rooting by minimal variance is the default

Select rooting method