NGS-Trex

NGS-Trex analyzes next-generation sequencing–derived transcriptomic data to reconcile gene trees with species trees and infer gene duplications, gene losses, and substitution-rate variation using the DLRS probabilistic model.

Key Features:

• Bayesian Analysis Framework: Implements a Bayesian framework to estimate posterior distributions over parameters including edge lengths and substitution rates.
• DLRS Probabilistic Model: Uses the DLRS model to integrate gene duplication, gene loss, and substitution processes in a unified probabilistic framework.
• Posterior Sampling of Reconciliations: Samples reconciliations from a posterior distribution conditioned on a species tree and corresponding gene sequences.
• Relaxed Molecular Clock: Models substitution-rate variation under a relaxed molecular clock to allow heterogeneous rates across lineages.
• Mapping of Duplication Events: Maps gene tree vertices to species tree edges or vertices to localize where gene duplications occurred.
• Input Requirements: Operates on a provided species tree and corresponding gene sequences as inputs for reconciliation and posterior inference.

Scientific Applications:

• Evolutionary Biology: Enables mapping of gene duplication and loss events on species trees to study genome evolution and the acquisition of new functions.
• Genomics and Transcriptomics: Supports analysis of next-generation sequencing transcriptomic profiles to relate gene expression data to evolutionary history.

Methodology:

Implements the DLRS probabilistic model within a Bayesian framework to estimate posterior distributions over edge lengths and substitution rates under a relaxed molecular clock, samples reconciliations given a species tree and gene sequences, and assigns gene tree vertices to species tree edges or vertices while accounting for gene duplication and loss.