FGF

FGF identifies and analyzes gene families using phylogenetic trees, duplication-fate assessment, and ka/ks selective-pressure calculations to study gene-family evolution.

Key Features:

• Phylogenetic Tree Visualization: Generates phylogenetic trees that display relationships among members of gene families.
• Gene Structure and Chromosome Position Information: Provides annotations of gene exon–intron structure and chromosome positions.
• Duplication Fate Analysis: Assesses outcomes of gene duplication events to characterize retention, loss, or divergence.
• Selective Pressure Assessment (ka/ks Calculations): Calculates ka/ks ratios (nonsynonymous/synonymous substitution ratio) to evaluate selective pressures on genes.
• Pseudogene Identification: Identifies pseudogenes that resemble coding genes within genomic sequences.
• Gene Structure Changes Detection: Detects alterations in gene structure such as exon loss, gain, or rearrangement.

Scientific Applications:

• Evolutionary analysis of gene families: Enables identification and comparative analysis of gene family expansion and divergence across genomes.
• Study of selective pressures and functional divergence: Uses ka/ks metrics to infer selection regimes and potential functional shifts among paralogs.
• Pseudogene and genome evolution studies: Supports detection of pseudogenes and structural changes to investigate genomic evolutionary processes.

Methodology:

Integrates genome sequence data to perform exhaustive searches for duplicated genes, constructs phylogenetic trees, annotates gene structures and chromosome positions, and calculates ka/ks ratios.