GeneSeqToFamily

GeneSeqToFamily generates gene trees and analyzes conservation of ancestral exon boundaries to investigate gene family evolution, identify ancestral duplication events, and detect divergence under positive selection using the Ensembl Compara GeneTrees workflow implemented within Galaxy.

Key Features:

• Gene Tree Generation: Generates gene trees from coding sequences to trace gene lineages and identify ancestral duplication events and genes that have diverged under positive selection.
• Exon Conservation Analysis: Assesses conservation of ancestral exon boundaries across multiple genomes to characterize structural changes within genes, providing more detailed insights than MSOAR, OrthoMCL, and HomoloGene.
• Ensembl Compara GeneTrees in Galaxy: Implements the Ensembl Compara GeneTrees pipeline as a Galaxy workflow to run the GeneTrees analyses within the Galaxy framework.
• Configurable Workflow: Supports modification of configurations and selection of different tools to tailor analyses and parameters for specific research needs.
• Visualization via Aequatus.js: Integrates Aequatus.js from the Aequatus software project to visualize gene families and their evolutionary relationships.

Scientific Applications:

• Evolutionary biology: Investigating how gene duplication contributes to morphological, physiological, and environmental adaptations.
• Homology and evolutionary trajectory analysis: Analyzing homologous genes and their evolutionary trajectories across multiple genomes.
• Detection of selection and novelty: Identifying genes that have diverged under positive selection and uncovering genetic bases of evolutionary novelty.

Methodology:

Generation of gene trees from coding sequences; analysis of ancestral exon-boundary conservation across multiple genomes; implementation of the Ensembl Compara GeneTrees pipeline within a Galaxy workflow; integration of Aequatus.js for visualization; configurable analysis via modification of workflow configurations and tool selection.