SwissTree

SwissTree provides a curated collection of 100 Gold Standard gene phylogenies and a consensus Tree of Life to benchmark and assess phylogenomic analyses and orthology predictions.

Key Features:

• Gold-standard gene phylogenies: Contains 100 Gold Standard gene phylogenies for benchmarking gene trees.
• Quest for Orthologs (QfO) affiliation: Developed within the Quest for Orthologs (QfO) initiative to improve and benchmark orthology predictions.
• Integrated species-tree sources: Leverages species-tree data from six projects: NCBI taxonomy, OpenTree of Life, the sequenced species/species ToL, the 16S rRNA database, Ciccarelli et al. (2006), and Huerta-Cepas et al. (2014).
• Reference organism coverage: The integrated species-tree projects collectively cover 147 reference organisms.
• Species-tree congruency metric: Reports that only 60% of possible splits in a dichotomous, rooted species tree are congruent across all examined species trees.
• Topological conflict localization: Identifies discrepancies at deep speciation events and within younger clades such as Hominidae, Rodentia, Laurasiatheria, and rosids.
• Prokaryotic inconsistency: Observes high inconsistency among evolutionary relationships of 27 archaea and bacteria.
• Large-scale gene-tree assessment: Assesses 458,108 gene trees from 65 genomes and finds consistent species topologies are more frequently supported than contradicting ones.
• Largest concordant species tree: Identifies a largest concordant species tree comprising 77 QfO reference organisms.
• Consensus Tree of Life synthesis: Synthesizes analyses into a consensus Tree of Life (ToL) used for benchmarking and integration with the Orthology Benchmarking web service.

Scientific Applications:

• Orthology benchmarking: Benchmark and evaluate orthology predictions using Gold Standard gene phylogenies.
• Phylogenomic database assessment: Assess the quality status of phylogenomic databases and track changes across database releases.
• Analysis procedure evaluation: Diagnose improvements following upgrades in analysis procedures.
• Species-tree congruency analysis: Evaluate congruency among species trees and identify topological conflicts across clades including Hominidae, Rodentia, Laurasiatheria, and rosids.
• Prokaryotic relationship evaluation: Assess inconsistency and conflict in archaeal and bacterial evolutionary relationships.

Methodology:

Compares species trees from six sources (NCBI taxonomy; OpenTree of Life; the sequenced species/species ToL; the 16S rRNA database; Ciccarelli et al. 2006; Huerta-Cepas et al. 2014) covering 147 reference organisms, assesses congruency of possible splits in dichotomous rooted trees, evaluates 458,108 gene trees from 65 genomes, and synthesizes results into a consensus Tree of Life.