OGtree 2

OGtree 2 reconstructs prokaryotic genome phylogenies by using overlapping genes (OGs) as conserved markers to infer evolutionary relationships among prokaryotic species.

Key Features:

• Overlapping Gene Utilization: Uses overlapping genes (adjacent genes with partially or entirely overlapping coding sequences) as phylogenetic markers because they are more conserved than non-overlapping genes.
• Distance-based Phylogenetic Reconstruction: Constructs genome trees using a distance-based algorithm that integrates both overlapping-gene content and gene order across whole genomes.
• NCBI Sequence Retrieval: Accepts genome accession numbers and retrieves complete genome sequences from the National Centre for Biotechnology Information (NCBI).
• Overlapping-gene Pattern Analysis: Identifies and compares overlapping gene patterns across genomes to quantify genomic similarity.

Scientific Applications:

• Evolutionary Studies: Facilitates analysis of microbial evolution and genetic mechanisms underlying speciation.
• Microbial Genomics Research: Supports comparative genomics and functional annotation of overlapping genes.

Methodology:

Users provide genome accession numbers; sequences are retrieved from the National Centre for Biotechnology Information (NCBI); overlapping gene patterns are identified and compared; and phylogenetic trees are generated using a distance-based algorithm that integrates overlapping-gene content and gene order.