HiDe

HiDe infers highways of horizontal gene transfer from unrooted gene trees and a rooted species tree to identify repeated gene-sharing routes among prokaryotic lineages.

Key Features:

• Highway Detection: Identifies pairs of species or lineages linked by highways of gene sharing where multiple genes are horizontally transferred between them.
• Input Data: Processes unrooted gene trees alongside a rooted species tree as inputs.
• Algorithmic Approach: Applies an improved algorithm to detect HGT highways and is reported to be robust to noise and high rates of HGT.
• Validation: Validated using both simulated and real-world datasets.
• Scalability: Capable of processing large datasets, demonstrated on a dataset comprising over 22,000 gene trees from 144 prokaryotic species.

Scientific Applications:

• Evolutionary Biology: Maps highways of gene sharing to infer evolutionary processes driving genetic diversity and adaptation in prokaryotes.
• Ecological Studies: Identifies patterns of HGT that inform past symbiotic and ecological associations among species.
• Genomic Research: Enables analysis of large phylogenomic datasets to study gene transfer events across extensive phylogenetic trees.

Methodology:

Uses unrooted gene trees and a rooted species tree as inputs, applies an improved algorithm to detect highways of horizontal gene transfer, and validates results on simulated and real-world datasets.