BIBI Introduction

leBIBI IV 16S Automated ProKaryotes Phylogenylogo LBBE

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leBIBI has allowed the phylogenetic positioning of unknown prokaryotes since 2002 with two major modifications in 2015 and this version since 2021.
The underlying software is complex because it incorporates parts of previous versions and also uses non-home-grown modules or software. It is also patchy. No upgrade from Linux or Python is possible without breaking the stable state, so the whole structure is obsolete.
YOU MAY USE leBIBI AS IT IS (no modification will be done, databases Dec 2022) AS LONG AS THE WEB-SERVER IS WORKING AND DON'T NEED TO BE UPGRADED (this will happen in 2025)

Note that the phylogenetic positioning is heavilly dependant of your data ESPECIALLY THE LENGTH of the sequence and the use of sequences under 800bp may return an extremely unreliable doubtful position. The set of methods used is also far from optimal when used with a query of less than 800bp.


The use of leBIBI must be done carefully, without over-interpreting the tree : the support values of the branches must be taken into account when interpreting the presumed position of the query.
Note that a support value below 0.95 has NO REAL value: the tree diagram is misleading in this case.


Do not trust too much what you see as this is only a 16S phylogeny (a very poor phylogenetic marker), especially if no full length SSU rDNA is available.
leBIBI does not identify a prokaryote! it allows you to visualize a phylogenetic tree of neighboring sequences, and only your expertise (in phylogeny and biology, by bringing together all the information) can do this.

One click mode: Submit your query

Query Format

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

OR #Genus_species:

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

Complementary DB

The default DB Contains Type Material (RT or T flag) and Prototypes (P or p flag) sequences. These sequences are selected on their quality and representativity.
Prototype sequences are selected when no Type Material is available. P flag is the sign of a better level of representativity. The p flag corresponds to species name with few sequences available or many sequences with high variability.

You may ask to add a limited number of sequences, taken the complementary DB, in the highest interest zone of the phylogenetic tree. This is not mandatory. Note that this may impairs the quality of the phylogenetic reconstruction

         

Results will not be conserved for more than 8 hours, if needed please download your working directory

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