Asteroid

Asteroid infers unrooted species trees from unrooted gene trees to reconstruct species relationships in the presence of incomplete lineage sorting (ILS) and high proportions of missing data.

Key Features:

• Robustness to missing data: Remains accurate with more than 80% missing data and outperforms ASTRAL and ASTRID in accuracy under high missing-data conditions.
• Handling of incomplete lineage sorting (ILS): Handles incomplete lineage sorting (ILS) during species tree inference.
• Efficiency: Achieves runtimes several orders of magnitude faster than ASTRAL on datasets with thousands of genes.
• Parallelization: Supports parallel computation to improve performance on large datasets.
• Support value computation: Computes support values for inferred species-tree branches.
• Flexible gene-tree inputs: Accepts multi-copy and multifurcating gene trees as input.
• Input/output: Infers an unrooted species tree from a set of unrooted gene trees.

Scientific Applications:

• Evolutionary biology: Reconstructing species-level relationships and investigating lineage diversification under ILS and missing data.
• Systematics: Inferring species trees for taxonomic and systematic analyses from complex gene-tree inputs.
• Phylogenomics: Analyzing large phylogenomic datasets containing thousands of genes and high proportions of missing data.

Methodology:

Infers an unrooted species tree from a set of unrooted gene trees.