Phylostems

Phylostems assesses temporal signal across individual clades within phylogenetic trees to support molecular tip-dating and the evaluation of heterochronous DNA sequence datasets.

Key Features:

• Clade-Level Temporal Signal Analysis: Assesses temporal signal within individual clades across a phylogenetic tree rather than only at the whole-tree scale.
• Extension of Root-to-Tip Regression: Applies the root-to-tip regression concept at clade-specific scales to evaluate temporal signal within subtrees.
• Identification of Tip-Dating-Appropriate Clades: Detects clades that exhibit sufficient temporal signal for downstream molecular tip-dating inference.
• Compatibility with Heterochronous Datasets: Operates on heterochronous DNA sequence datasets sampled at different times to assess temporal signal for rate and time estimation.

Scientific Applications:

• Molecular Tip-Dating: Evaluates whether heterochronous sequence datasets contain sufficient temporal signal prior to conducting tip-dating analyses to estimate evolutionary rates and divergence times.
• Branch-Specific Temporal Inference: Provides a more granular assessment of temporal signal across branches to inform analyses of evolutionary timelines within different clades.

Methodology:

Extends root-to-tip regression by performing clade-specific temporal signal assessments on phylogenetic trees derived from heterochronous sequence datasets.