FLAVi

FLAVi annotates complete and partial genomes of the family Flaviviridae (including dengue, hepatitis C, West Nile, yellow fever, and Zika viruses) to identify coding loci and enable comparative genomics and phylogenetic analyses.

Key Features:

• Annotation Framework: Provides an annotation framework tailored for Flaviviridae, encompassing the genera Flavivirus, Hepacivirus, Pegivirus, and Pestivirus to manage gene content variation.
• Ab Initio and Homology-Based Strategies: Integrates ab initio prediction methods and homology-based strategies, recovering 100% of genes in Flavivirus and Hepacivirus genomes and near-complete recovery in Pegivirus and Pestivirus.
• High Accuracy: Reports no false positives during annotation, ensuring high precision of locus assignments.
• Phylogenetic Analysis Enhancement: Enables combined phylogenetic analysis of multiple genes with data partitioning and outgroup inclusion, improving tree topology and congruence compared to analyses without outgroups or partitioning.

Scientific Applications:

• Phylogeny reconstruction: Constructs updated, multi-gene phylogenies of Flaviviridae to resolve evolutionary relationships.
• Monophyly testing: Enables testing of ingroup monophyly among virus lineages within Flaviviridae.
• Lineage relationship elucidation: Clarifies relationships among virus lineages and supports analyses such as the close relationship between dengue and Zika viruses.

Methodology:

Annotation combines ab initio prediction and homology-based strategies, and phylogenetic analyses use combined multi-gene datasets with data partitioning and outgroup inclusion.