STRAW

STRAW reconstructs species trees from collections of gene trees using coalescent-based methods for phylogenetic inference.

Key Features:

• MP-EST: Implements the MP-EST coalescent-based species tree estimation method using rooted gene trees.
• STAR: Implements the STAR coalescent-based species tree estimation method using rooted gene trees.
• NJst: Implements the NJst coalescent-based species tree estimation method using unrooted gene trees.
• Gene tree input types: Accepts collections of rooted gene trees for MP-EST and STAR or unrooted gene trees for NJst.
• Coalescent-based multilocus analysis: Uses coalescent-based approaches to accommodate coalescence events across multilocus datasets.
• Species tree output: Generates an estimated species tree from input gene trees.
• Modified Robinson-Foulds distances: Computes modified Robinson-Foulds distances between individual gene trees and the estimated species tree to quantify dissimilarity.
• Tree comparison visualization: Produces visual comparisons of gene trees with the estimated species tree.

Scientific Applications:

• Evolutionary biology: Infers species relationships under coalescent models for evolutionary biology research.
• Conservation genetics: Provides species tree estimates applicable to conservation genetics analyses.
• Comparative genomics: Supplies species tree frameworks for comparative genomics of multilocus datasets.
• Gene-tree congruence assessment: Assesses congruence among gene trees and the estimated species tree using modified Robinson-Foulds distances.

Methodology:

Implements the coalescent-based methods MP-EST, STAR, and NJst; accepts rooted gene trees for STAR and MP-EST and unrooted gene trees for NJst; computes modified Robinson-Foulds distances and provides visual comparisons between gene trees and the estimated species tree.