Current version (2016/sep/29) is BIBI_DB V31.0

Welcome to leBIBI’s Documentation!

leBIBI-QBPP

The Quick Bioinformatic Phylogeny of Prokaryotes is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence (the submission of batches of sequences is also possible). leBIBI QBPP is also giving the useful informations on species identification if it is needed.

leBIBI-PPF

The new evolution of the engine, leBIBI-PPF is now available. It enables to reconstruct SSU-rDNA (16S) driven phylogenies of the prokaryotes on the fly. The WEB interface allows to submit a list of (nomenclature levels-databases) and to collect the corresponding sequences. The leBIBI-PPF engine then seach the sequences that are closely-related to each member of the list on the basis of a similarity BLAST search and reconstruct the phylogeny of the set of the query including the recruited sequences. The last step uses a simple phylogenetic tree-viewer and taxonomy-level oriented editor.

leBIBI-PPF Step by Step is the best way to begin.

LeBIBI-PPF is also useful to get a phylogenetical view of the outputs of NGS-microbiome studies.

Note

Recently the nomenclature used by NCBI Taxonomy has evolved. In some cases the Genus name is surrounded by brackets like here :[Clostridium] fimetarium This is incompatible with some parts of the leBIBI-QBPP engine. Temporarily the brackets have been replaced by . so that the names appears like : .clostridium. fimetarium. As the genus is not correct (this species belongs to the genus .Lachnoclostridium.), the capital has been suppressed.

Contents:

Indices and tables