PhEVER

PhEVER provides a curated database of homologous protein families, multiple sequence alignments, and phylogenetic trees compiled from 2,426 non-redundant viral genomes, 1,007 non-redundant prokaryotic genomes, and 43 eukaryotic genomes to support analyses of viral evolution and virus–host and virus–virus lateral gene transfers.

Key Features:

• Homologous family compilation: Clusters proteins derived from viral and cellular sequences into homologous families that each include at least one viral sequence.
• Genome coverage: Incorporates data from 2,426 non-redundant viral genomes, 1,007 non-redundant prokaryotic genomes, and 43 eukaryotic genomes spanning plants to vertebrates.
• Multiple sequence alignments: Provides alignments for each homologous protein family.
• Phylogenetic trees: Provides phylogenetic trees for each homologous protein family to infer evolutionary relationships.
• Focus on lateral gene transfer: Enables identification and analysis of virus–virus and virus–host lateral gene transfers across viral and cellular homologs.

Scientific Applications:

• Analysis of lateral gene transfer: Enables detection and evolutionary analysis of virus–virus and virus–host lateral gene transfers.
• Phylogenetic inference: Supports reconstruction of evolutionary relationships among viral proteins and their cellular homologs.
• Study of viral adaptation and emergence: Facilitates investigation of acquisition of novel functions by viruses relevant to viral adaptation and emerging infectious diseases.

Methodology:

Protein sequences from completely sequenced genomes were clustered into homologous families, and multiple sequence alignments and phylogenetic trees were generated for those families.