TREEasy

TREEasy automates the inference of gene trees, species trees, and phylogenetic networks from multilocus genomic datasets for evolutionary and systematic analyses.

Key Features:

• Automated Sequence Alignment: Performs sequence alignment using MAFFT.
• Gene Tree Inference: Infers gene trees using IQ-Tree.
• Species Inference from Concatenated Data: Performs species inference on concatenated data using IQ-Tree and RaxML-NG.
• Species Tree Inference from Gene Trees: Infers species trees from gene trees using ASTRAL, MP-EST, and STELLS2.
• Phylogenetic Network Inference: Constructs phylogenetic networks using SNaQ and PhyloNet.
• Implementation: Implemented in Python.

Scientific Applications:

• Staghorn coral evolution: Reproduces existing analyses of staghorn coral evolutionary history.
• WGD clade of yeast: Investigates evolutionary patterns in the "WGD clade" of yeast and can uncover novel relationships.

Methodology:

Performs MAFFT alignment, infers gene trees with IQ-Tree, conducts species inference from concatenated data with IQ-Tree and RaxML-NG, infers species trees from gene trees with ASTRAL, MP-EST, and STELLS2, and infers phylogenetic networks with SNaQ and PhyloNet; requires FASTA files and nine parameters as inputs.