This unify the databases building work and as riboDB is a long-term project of our team, this optimize the sustainability of leBIBI. Some options has been deleted because of their complexity and limited usefullness (currently some to-be-suppressed functions are not working).
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 No upgrade from Linux or Python is possible without breaking the stable state, so the whole structure is obsolete.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 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. After a new set of tests I confirm that the results using a sequence length under 400 Bp are mostly faulty and when under 800 Bp you should ALSO have to consider the BLAST results as a safety rule. Consequently, in the "one click mode", THE LENGTH OF THE SEQUENCE MUST BE >400 BASES. Note that this is MANDATORY and will not be modified
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.
