leBIBIpqp

leBIBIpqp reconstructs phylogenetic relationships of prokaryotic (Archaea and Bacteria) nucleotide sequences to estimate species-level taxonomic positions.

Key Features:

• Input Markers: Accepts nucleotide sequences from reference markers SSU rRNA, rpoB, and groEL2.
• Automated Sequence Retrieval and Alignment: Automatically retrieves closely related sequences from its reference databases and aligns them.
• Phylogenetic Reconstruction: Employs an approximate maximum likelihood approach for tree inference.
• Quality Parameters and Taxonomic Assignment: Returns a set of quality parameters for each analysis and suggests taxonomic assignments when possible.
• Reference Databases: Uses reference databases extracted from GenBank that reflect current bacterial nomenclature and indicate species origins, provided at four degrees of stringency from "superstringent" (one type strain per species) to "lax".
• High-Throughput Capability: Can analyze anywhere from one hundred to over a thousand sequences in a single run.

Scientific Applications:

• Clinical Microbiology: Identification of bacterial and archaeal pathogens from sequence data for diagnostic and epidemiological purposes.
• Industrial Microbiology: Identification and characterization of microorganisms used in industrial and biotechnological processes.
• Environmental Microbiology: Exploration of microbial diversity and phylogenetic placement of sequences from environmental samples.
• Specialized Research Laboratories: Phylogenetic placement and taxonomic inference to support targeted research investigations.

Methodology:

Reference databases are extracted from GenBank with four degrees of stringency; the system automatically retrieves closely related sequences, aligns them, reconstructs phylogenies using an approximate maximum likelihood approach, and returns quality parameters and suggested taxonomic assignments.