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Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Updated: Nov 7, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Root Digger: a root placement program for phylogenetic trees.

Ben Bettisworth¹, Alexandros Stamatakis^2,3

¹Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. ben.bettisworth@h-its.org.

BMC Bioinformatics

|May 2, 2021

Summary

This summary is machine-generated.

RootDigger software identifies the most likely root location on phylogenetic trees using non-reversible Markov models. This tool aids in interpreting evolutionary relationships and quantifying rooting uncertainty.

Keywords:

Maximum likelihood Phylogenetic analysis Phylogenetic rooting

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Computational Biology
Phylogenetics
Evolutionary Biology

Background:

Phylogenetic analysis commonly infers unrooted trees, but root identification is crucial for downstream interpretation.
Existing methods for rooting include molecular clock analysis, midpoint rooting, and outgroup rooting.
Non-reversible Markov models offer a probabilistic approach to evaluating root positions.

Purpose of the Study:

To introduce RootDigger, a novel software for determining the most probable root location on phylogenetic trees.
To assess the confidence of root placements using a non-reversible Markov model.
To provide a tool for quantifying and explaining uncertainty in phylogenetic root inference.

Main Methods:

Utilizes a non-reversible Markov model to calculate the likelihood of root positions on a given tree.
Compares RootDigger's performance against established rooting tools like IQ-TREE and MAD.
Employs an exhaustive mode to quantify and explain rooting uncertainty.

Main Results:

RootDigger successfully identifies root locations on phylogenetic trees.
The software demonstrates comparable or superior performance to existing tools (IQ-TREE, MAD).
RootDigger's exhaustive mode effectively quantifies and explains uncertainty in root placement.

Conclusions:

RootDigger is a valuable tool for rooting existing phylogenies and assessing root placement uncertainty.
The software is freely available under the MIT license.
RootDigger enhances the interpretation and reliability of phylogenetic analyses.