RootDigger

RootDigger infers the most likely root position on unrooted phylogenetic trees using a non-reversible Markov model to compute likelihoods and provide confidence values for root placements.

Key Features:

• Non-reversible Markov model: Uses a non-reversible substitution model to evaluate root positions on a phylogenetic tree.
• Likelihood-based scoring: Computes likelihoods for candidate root placements on a given unrooted tree.
• Confidence estimation: Assigns a confidence value to each possible root placement to quantify certainty.
• Root identification: Identifies the most probable root location based on likelihood comparisons.

Scientific Applications:

• Root inference without suitable outgroups: Provides an alternative rooting method when midpoint rooting or outgroup rooting are unsuitable or insufficient.
• Downstream phylogenetic analysis: Supplies statistically informed root placements to improve interpretation and downstream evolutionary analyses.

Methodology:

RootDigger employs a non-reversible Markov model to compute likelihoods for candidate root positions on an input phylogenetic tree and assigns confidence values to each placement.