msc_tree_resampling

msc_tree_resampling implements gene-wise resampling to quantify branch support for clades inferred on species trees from gene-tree datasets within multispecies coalescent (MSC) two-step coalescent analyses.

Key Features:

• Gene-wise Resampling: Implements gene-wise resampling that resamples genes rather than sites to preserve gene-tree estimations.
• Bootstrap and Jackknife: Employs bootstrap and jackknife statistical methods to assess clade support under gene-wise resampling.
• Compatibility with Coalescent Methods: Supports downstream coalescent inference with ASTRAL, MP-EST, NJst, and STAR.
• Resampling Recommendation: Recommends gene-wise resampling over site-wise or combined gene+site resampling due to superior performance in maintaining gene-tree integrity.
• Empirical Validation: Validated using data from three empirical phylogenomic studies, producing more conservative clade support than site-wise bootstrap analyses.

Scientific Applications:

• Phylogenetic Inference: Quantifies branch support on species trees for multispecies coalescent phylogenomic studies and two-step coalescent analyses.
• Conservative Support Estimation: Provides conservative support estimates to reduce the impact of gene-tree estimation errors on species-tree conclusions.

Methodology:

Performs gene-wise resampling and applies bootstrap and jackknife techniques, explicitly contrasting gene-wise resampling with site-wise resampling regarding gene-tree-estimation error.